Deamon, the issue with stacking batteries as I understand it is that the battery closest to the coil is going to drain faster than the other battery. If it becomes too drained the other battery can see too much current draw causing it to heat up. A protected device does not protect you from this as far as I know. Please correct me if I'm wrong here.
If I were going to stack batteries, this is what I would do:
Start with new sets of batteries, same make and manufacturer.
Keep my batteries in pairs. Mark the first pair of batts 'A1' and 'A2'. The second pair 'B1' and 'B2'.
Do not discharge lower than 3.4 volts each before re-charging. The mod does not know each battery's voltage, just the voltage of the stacked pair, so you will have to take the batts out and check with a multi-meter.
Take batts out, check and note the sequence. Say '1' was on top and '2' on the bottom.
If there is more than 0.2 V difference between them I would retire the pair. They can then be used by themselves.
After charging the batteries check the voltage. They should be within 0.1 V of each other. More than this and I would retire them.
Replace batteries in reverse order into mod. So in this case, '2' goes on top and '1' on the bottom.
Again, if you know more about this than I do, please let me know. I don't stack so I never did much research on it. My opinion is just from what I've picked up on from general reading.