Hi,
I thought maybe I should chime in here - perhaps I can answer a couple questions and/or reduce some confusion about batteries. I am not a battery "expert", however I do have significant experience with them especially in the RC hobby field where a variety of battery types are used that are of high capacity and capable of fast discharges.
The 4.2v phenomena: Li-Ion and Li-Poly batteries are rated at a nominal 3.7v. Like any other battery, as the battery charges, its voltage goes up. 4.2v per cell is the magic number for these kinds of batteries however. Lithium batteries can be very hazardous, and overcharging one can make it explode. Chargers for these batteries must never exceed the 4.2v in the batteries. The beauty of these batteries in use however, is that the voltage holds higher longer than other batteries (such as NiMH). The voltage still drops under load however, but draining towards the end of the battery capacity you will find the voltage starts to plummet. You must be careful here because if the voltage of a cell gets too low, it damages the cell. A damaged cell does not hold as much charge, might not accept a charge anymore, and/or can explode when you try to recharge it. In the Li-Poly world, most people suggested cut-off at 3.0v. Today there is a trend of making this slightly higher (3.2v, maybe even 3.4v). Because the voltage drop-off at the end is so fast, the impact on "usage time" is negligible for a bigger increase in safety and battery care. This is especially considered in multi-cell applications (7.4v, 11.1v, etc) because....
Very often (read almost always), cells stacked in series will discharge at different rates. Sometimes "matched cells" can be obtained together that help alleviate this. The problem is twofold.
1- Capacity: Battery capacity varies slightly from battery to battery to begin with, and also capacity typically drops after a number of cycles. If you have two Batteries from the same pack, use one of them for a couple months, and then charge them both up, the one you have been using will have a slightly lower capacity. This means if you now discharge them at the same rate, the one you have been using will reach the magic cut-off voltage first.
2- Internal Resistance: Batteries often vary in the internal resistance. this means that even if you have two batteries that you precisely measure to have the same capacity, they will likely have slightly different internal resistance. This will cause a slight difference in discharge anyway.
What this means to you, is that very often (again, read almost always) you will find that if you have 2 of these batteries stacked in series for higher voltage, one of them WILL reach the cut-off voltage before the other. The other one will possibly read a higher voltage that "looks okay", but that does not mean it has a significant charge left in it. Remember Li batteries are designed to hold maximum voltage throughout their discharge cycle, and only drop significant voltage (plummet really) at the very end of their usable capacity.
So, discharging batteries till one cuts off and then just replacing one? Bad idea. Charge them both.
Swapping positions of the two batteries? Should not make any difference - it is purely a function of capacity, internal resistance, and discharge rate, not whether one is on top of the other or vice-versa.
Should you wait until the cut-off to charge them? You can. But you can charge them more frequently, not letting them discharge as far. This in fact seems to prolong the life of these kinds of batteries. The diminished battery capacity from 100 full cycles (full charge, full discharge) is greater than that of 100 half cycles (full discharge, half discharge).
I hope this helps to clear up some of the confusion. If I forgot to address something, let me know
