Using a Y on ailerons or flaps works. You need to take care that the control horns and linkages are installed identically so that each of the surfaces move identically. That will be harder to do with the flaps since both servo arms will have to be pointing in the same direction making the linkages somewhat different right to left. Personally I prefer to use separate channels so that I can adjust the neutral and end points separately.

What's wrong with a set up like this? :
1 throttle (ECU)
2 elevator
3 rudder with matchbox to steering
4 right aileron
5 left aileron
6 right flap
7 left flap
8 retracts
9 brakes

A good 5 cell pack fresh off the charger can be at or slightly above 7 volts. In that case it is possible to get some slight servo jitter when you first turn on. If that happens all you have to do is wiggle the transmitter sticks a few times. That will drop the pack voltage by a few tenths of a volt, the jitter stops, and you are ready to fly. As I said before I have unregulated 5 cell nicad packs in all of my planes and never have had an issue in thousands of flights. You have to use servos that can take the extra voltage, and you are. All of the JR servos I've used work fine.

If using two batteries makes you feel better then by all means do so.

Joe