In theory two "identical" packs on two "identical" regulators should drain evenly. I have a couple of models set up this way with dual Tech-Aero regs and FP 350's and it has never happened, although they are pretty darned close.

Using a matched set of batts/regs removes some of the intangibles, at least in my unsophisticated little electronics mind. If the draw-down is within a couple tenths of a volt after 5 flights, close enough.

What is much more important is to use a battery checker that can check loaded voltage, i.e. voltage with a .5-amp or 1-amp load to ensure that the cells are good, and to check the IR's of the cells when recharging. These checks are the only real indicators of cell health. Unloaded voltage can be very misleading.