What can happen is if the gear bends and gets hung up; ie can not fully retract the servo is constantly drawing current attempting to zero itself. Use a good 6 volt battery and check your gear function every flight. Also ensure when you initially set it up that you set the EPA ((End Point Adjustment) must have a computer radio to do this) so that it is not trying to over retract or extend the gear.

Now to answer your question; yes, you can set up a battery for your retracts. First off you need to know what the three wires for your servos are. If you run Futaba gear the white wire is for signal, black ground and red is positive (4.8-6.0v). With Hitech and JR the signal wire is Yellow, ground is brown, and positive is red. Do not cut these wires. Get a 12-24 inch servo extention to plug into your reciever and another "on/off" switch. Cut the pos and neg wires on the extention and splice in the on off switch. Attach a battery to this switch as normal. The signal will still come from the reciever but power will not be drawn from your main battery.

EDIT//

I have modified the scematic to the specs Pettit mentioned.