First of all, the Tritons available now have the revision on the software dealing with Lipo's. The problem was with memory settings and even my old Triton (from January) will charge Lipo's in manual mode.
Secondly, no its not alright to leave your reciever on just "twitching" the servos. This is neither good for the servos or your plane and causes unnecessary wear and tear on everything. You will most likely find something failing on you at the worst possible time and gravity is not kind.
If your batteries are NMH don't even worry about discharging them. Charging at a C/10 rate will not harm your batteries if you go over by a couple hours here and there. If your batteries are nicads then just discharge them with a flashlight bulb or automobile bulb (aprox 3-400mA/h drain) until bulb is dim. Completely draining the batteries is not a good practice either...try to leave about 1v/cell. Hope this helps