[bodywerks]

The failsafe mechanism uses the signal and ground wire to control the on/off, where an open circuit between the two turns the system on, and a closed circuit turns the system off. So you need to modify a 3-wire switch, or a two wire switch so that the positive lead is where the signal lead would go. Not a big deal. Many people actually use a simple servo extension that plugs into a charge jack and they use a Spektrum bind plug as their switch - install the bind plug to turn the system off and remove it to turn it on. But I assume the whole reason you want to use something other than the pin/flag switch is because you don't want to have to keep track of the pin all the time(?), in which the bind plug idea still has you in the same boat.
And yes, you can use the system with only one battery plugged in, but you are losing the advantage of battery redundancy and the failsafe features incorporated into the PE pro, but you know this.