Edit: see also Is soldering wires directly on a NiMh battery safe?
nothing in there that I could see that would 'balance' them
This may be why they don't last very long.
Due to manufacturing variance, one of the batteries will go flat first while the others have more charge. This can result in current being driven through it by the others while it's flat, damaging the battery. Or the reverse happens while charging: one will fill up first, and then suffer overcharge damage. Does the charger automatically stop on full charge or it it timed?
It may be better to adapt the battery holder to the batteries with a saw, so you can use the holder and charge them individually.
Or look for cheap repurposeable packs, eg. http://www.dx.com/p/gd-509-2-4v-1200mah-rechargeable-2-x-aa-cordless-phone-replacement-battery-pack-white-292547#.VIXLYsmfjjU is clearly 2x AA heatshrunk together, you may be able to find 4 heatshrunk together in the right format then just change the connector.
Edit 2: by the way, I would put money on the tanks suffering mechanical failure or enemy action before the battery packs become an issue. Unless they're expensive 'models' rather than 'toys'.
I wouldn't connect any battery to your phone but the one designed for it. The charging circuit is designed for the specific battery.
You can technically probably connect a Li-Ion and LiPo battery in parallel with a properly designed charger, but it is not recommended. Usually only identical cells are connected in parallel or series.
One big issue is current hogging in the constant-current charge phase. Initial charging of a lithium ion battery is done at constant current, generally expressed as some rate like "1C" which means charging a 2500 mAhr battery at 2.5 amp (i.e., a one hour charge rate). If you put two cells in parallel, you might think you could increase the charge rate, but unless the cells are identical, one of them may hog most of the current. So if you are charging with 5A, it might be that 1.5 amp goes to one battery and 3.5 amp goes to the other: exceeding it's safe limit.
Another issue is with charging voltage. Lithium ion chargers switch to constant voltage mode when the battery gets to a certain pre-set voltage, nominally 4.2 volts. However, different anode types have slightly different voltages, in the 4.1-4.2 range. If you look at the data sheets for li-ion charging circuits, they usually have some mode selection to trim the voltage for slightly different cell types. If you connect two batteries with different voltages in parallel, you could overcharge one.
Finally, lithium ion chargers are designed to stop charging when the constant voltage phase drops to a certain minimum current to avoid trickle charging, which will cause overcharging and cell damage. If you put batteries in parallel, that threshold needs to be adjusted. If the batteries are not identical, that could be off.
In practice, if you set your charger to charge at the rate of the smaller cell, and you make sure that the maximum voltage of the two cells is the same, nothing bad is likely to happen. However, charging will take about twice as long as if you used identical cells, so this is not usually done. Multi-cell battery packs are usually made from brand new identical cells ideally from the same manufacturing lot, and permanently connected so that they age together.
Best Answer
From the title it seems you're concerned that the two three-cell packs will total 3.6 V each and the one two-cell pack will put out 2.4 V. Connecting eight 1.2 V cells in series will give you 9.6 V. It makes no difference that they are in different packs. Think of the internal connections in the holders, and the wires between the holders, all being zero ohms. The physical grouping of the cells makes no difference to the total voltage.