How to combine batteries in series and parallel
Don't connect batteries in parallel unless you wish to have trouble - if one battery fails it will discharge the one in parallel with it and likely damage that good battery and may even cause a fire or explosion depending on battery type.

Connect all the batteries in series and if the voltage you desire is not what the battery voltage gives use a buck converter to reduce the voltage to what you want. Buck converters of this type can be over 95% efficient at converting power to a different voltage level and they hardly take up any room and I bet you can get one off ebay for a really tiny fistful of dollars (The Clint Eastwood reference I apologize for LOL).

All is not sweetness and light even with them in series - over-load currents can cause cell reversal especially in NiCd cells but, this can also happen in parallel configurations.