Mikvah Construction
By Rabbi Schneur Zalman Lesches 

Techniques 
It is both impractical and unhygienic to build a mikvah with a solitary bor (reservoir) of kosher rainwater. One would have to wait until it rained forty se'ah (a volume of measure) in order to refill the mikvah to change the waters. This is especially difficult in places where there is no rain in the winter.

The most practical solution is to build a mikvah with two (or more) boros. One bor becomes the bor hatvilah (immersion pool), while the other contains natural rainwater. This technique enables us to clean the mikvah water without having to wait for rainfall.

There are three ways to build the bor that holds the natural rainwater: Hashoko, Zriah and Bor al gabai bor

Hashoko:
Hashoko means to "kiss", i.e., contact and touch.  Two boros are built side by side.  One is filled with rainwater valid for immersion.  The other is filled with tap water initially not valid for immersion.  Only when the ordinary water comes in contact with the rainwater does it become valid. The bor filled with ordinary water is thereby rendered kosher for ritual immersion.
 Thus:
(a) If there is a hole between the boros and the waters contact each other, or
(b) The waters meet at the top, over the rim of the boros then both boros are kosher.
The hole must be higher than the forty se'ah of rainwater in the bor hashoko.   In the bor hatvilah, it must be below the water level.  As the water level must be approximately 120-125 cm. (47-49 inches) above the ground, the hole must be lower than 120 cm.
 The hole where the waters meet must be as wide as a shfoferes hanod - two average fingers that fit inside and turn easily.
 How can one determine whether a mikvah uses the hashoko method?  If upon investigation it is found that no city water flows into the rainwater bor - it is identified as a bor hashoko.
When changing the water, one empties the bor hatvilah and the bor hashoko remains full of valid waters.  Then the bor hatvilah is filled with fresh water, and when the waters meet at the hole connecting the boros, the added tap waters attain the qualification of the bor hashoko.
Sometimes a stopper is inserted into the hole before emptying the mikvah, so that as much original rainwater as possible is retained.  However, this stringency can later cause complications.  If one forgets to unplug the stopper after refilling the bor hatvilah, then any immersions in this mikvah are invalid, because the ordinary water never touched the rainwater and therefore did not achieve its validity.  Hence, some opinions prefer not to use a stopper at all, even though this means losing some of the original rainwater.
There are varying opinions among Halachic authorities as to whether the hole must stay open once the hashoko has been made.  Some are of the opinion that the hole should be closed for, during immersion, some water is pushed through the contact hole back into the bor hashoko and becomes zoychalin, flowing (even from one bor to another) thus rendering the mikvah unfit. 
The Chabad custom follows the ruling of Rabbeinu Yeruchim, that the hole must be open at the time of immersion for the water to retain the qualification of the rainwater bor.  However, during immersion, even a small hole suffices (kol shehu).  Shfoferes hanod is only needed for the initial contact. 
If a stopper is used, one must be careful not to use materials that can be mekabel tumah (li. "accepts ritual impurity") Anew wooden stopper is the best choice. It is preferable not to use a rubber or plastic stopper. A metal stopper should definitely not be used. The following are some disadvantages of the hashoko method:
This technique is not foolproof.  It is possible that whoever fills the bor hatvilah will not use enough water to reach the hole connecting the two boros
 Additionally, in a place where a stopper is used before emptying the bor hatvilah, the attendant can forget to remove the stopper after refilling the mikvah.
 In either instance, since the ordinary tap water in the bor hatvilah did not contact the validating hashoko waters, the waters in the bor hatvilah remain invalid for immersing.  This causes serious Halachic problems when people have immersed in such a mikvah.  A competent Rabbi should immediately be contacted.
 Another disadvantage is that the water in the bor hashoko often sits undisturbed for long periods of time and becomes stagnant.  The structure of the bor zriah solves these problems. 

Zriah:
Translation of zriah is "sowed", like grain, "sown" into the ground.Forty se'ah of rainwater is gathered in a bor, to which tap water is added.   The tap water intermingles with the rainwater as one body of water, and attains the qualification of the original rainwater.  The water then overflows through an outlet (hole) into the mikvah stopping at the necessary level.
Hence, the tap waters are "sown", making them valid for immersion - equal to rainwater.
 The advantage of the zriah method is that the ordinary tap water becomes kosher immediately as it enters the bor and makes contact with the rainwater.  Unlike the hashoko method, the zriah technique does not have to wait for a minimum level and for the waters to meet in order to be considered a united body of water, nor is there a stopper.  Once the bor zriah is filled with rainwater the mikvah is valid and almost foolproof.  The Rabbi supervising the mikvah has no reason to worry whether the mikvah waters are connected to the bor or if the attendant remembered to remove the stopper.
 Another advantage: The water in the bor zriah changes often and remains fresh.
 A typical mikvah using the zriah method has two adjoining boros with a hole connecting them at the top.  The hole must be higher than the forty se'ah of rainwater in the bor zriah.  In the bor hatvilah, it has to be higher than the water level (approx. 140 cm. (56 inches) from the floor).  The waters do not mingle during immersion.
Thus:
1. Begin by filling the bor zriah with a minimum of forty se'ah of rainwater.
2. Add tap water into the rainwater bor, preferably in a way that the waters enter at a level lower than the connecting hole (the hamshocho process is nonetheless above water level).
3. When the water level is high enough, the water will pour through the hole into the bor hatvilah.
4. The waters in the bor hatvilah are valid when the bor contains at least forty se'ah and the water level is high enough for immersing.
     How can one determine whether a mikvah uses the zriah method?  If upon investigation it is found that the city water flows into the rainwater bor and then into the bor hatvilah - it is identified as a bor zriah.
 Though more reliable than the hashoko method, the bor zriah is still prone to problems.  It is common practice to drain the mikvah by using an electric pump that does not completely drain all the water.  Occasionally, when the pump is turned off, some water may return into the mikvah from the pump, sheuvim (lit. "drawn waters", waters that are invalid for a mikvah via containment in a vessel).

Additionally, the mikvah maintenance attendant may sometimes choose to remove the remaining traces of water with a sponge or bucket. Water from the sponge or mop will drip back into the mikvah, sheuvim, as a matter of course.

Then also, the mikvah may be washed with water from a bucket (sheuvim) and some water may be left in the mikvah. In these cases, the remaining water is considered sheuvim - with qualified kosher waters from the bor zriah, the three initial luggin (a liquid measure used in the times of the Mishna) of remaining water - whether from the pump, mop or pail - preceded the "valid" water and invalidates the mikvah.

Bor Al Bagai Bor
As explained in previous sections, a mikvah usually contains two boros - one filled with rainwater, the other with tap water. Generally, there are two ways the boros can be constructed:

1) Two boros are constructed side by side with a common wall.  On the common wall a hole is placed higher than the height of forty se'ah.  One bor is filled with forty se'ah of rainwater. The other bor is filled with tap water until the waters make contact and intermingle with each other, rendering the water in the bor hatvilah kosher for immersing.
2) a mikvah be built bor al gabai bor, literally, "one bor on top of another bor".  This mikvah is constructed in the following manner:
a) A single deep bor is built during construction.
b) A divider of cement is built, forming an upper bor and a lower bor.  The walls below the divider can project into the bor to support the divider, or a keyway can be formed in the wall and the divider cast into it.  The divider serves as a floor for the upper bor and a ceiling for the lower bor.
c) The upper bor becomes the bor hatvilah.  Steps are built for the user to descent and immerse.
d) The lower bor contains [two times] forty se'ah.
e) An opening is left in the divider large enough for a person to pass through; then it is closed with a cover panel.  There are two holes, each measuring a square tefach (handbreadth).
The holes unite both bodies of water; tap water in the upper bor unites with the lower rainwater, giving the ordinary water the needed validation for immersion.
Why two holes?  Some suggest that there be a second hole in case one of them becomes blocked.  This can occur when the person immersing places a foot in the hole, preventing the waters from remaining united.  Building a second hole guarantees constant contact between the boros.  The holes are therefore built apart from each other, to ensure that the feet of the person immersing cannot block both holes simultaneously.
There are no holes or drains in the lower bor where the rainwater is deposited.
How can one determine whether a mikvah uses the bor al gabai bor method?   If upon investigation it is found that there are two holes in the floor of the mikvah, leading to the bottom bor, it is identified as having been built bor al gabai bor.
This mikvah is constructed preferably with the tap water flowing directly above one of the holes.  When filling the mikvah, rainwater pours into the lower bor until it is full.  Ordinary water is then added through the hamshocho (a procedure where waters run across an area of soft ground or cement) method into the upper bor hatvilah directly above either hole, as in the zriah method.
The procedure is different if the tap water does not flow directly over the holes.  First, fill the lower bor with rainwater until it overflows and covers the floor of the upper bor.  Then, add ordinary water into the upper bor.  Since the rainwater preceded the tap water, this is also a form of zriah.  Now the mikvah is valid and ready to be used.  When the waters of the upper bor become dirty one need only to pump out the upper bor and refill it.
The advantages of this unique method are clear:
Unlike the side bor hashoko technique, there is no need to wait for the waters in both boros to come into contact with each other nor is there any need for a stopper.  Once the lower bor is filled with rainwater the mikvah will be valid and foolproof.  The Rabbi supervising the mikvah is secure in the knowledge that the mikvah is valid without worrying whether the waters met at the hole or whether the attendant may have forgotten to remove the stopper.
Similar to the zriah method, where tap water flows directly into the rainwater and is considered "sowed into the ground", this is also considered zriah in its best possible form.
One additional, but very significant advantage is the fact that the upper section is a continuation of the rainwater bor.  The square tefach hole(s) dismiss, Halachically, the presence of the divider.  Therefore, when one is immersing in such a mikvah, they are in actuality, immersing in the rainwater bor itself.
Therefore, if one has a mikvah constructed with the method of bor al gabai bor, there is no need for additional side hashoko or zriah boros.

This excerpt on the three types of mikvah is taken from "Understanding Mikvah" by Rabbi Schneur Zalman Lesches. For further information on the building of a mikvah, or further understanding of the differences of construction and why some prefer one method over another, please consult the book in its entirety.