Servo Controller Board with 2 Power Supplies

[butters]

Hi guys, I've been working on this board for awhile now and it's basically designed to control a quad 2-input multiplexer (74AC157MTC) to switch between an external set of servo control signals (coming from another board) and servo control from the on-board ATMega1281.  The board has to be reduntantly powered (it's essentially a failsafe system) with its own little battery (I'm gonna use a single cell LiPo), but I am at odds with how to deal with the servo power lines.  The servos are powered by their own high-capacity 5V NiMH battery and will pull quite a few amps at times.

I initially thought that I would be able to power the servos seperately from the board with their own battery as long as I keep a common ground between the two voltage sources, however some preliminary testing is suggesting that this won't work.  Is having the servo control signal driven by a different voltage source from the servo power source going to be an issue when I try to control the servos with the on-board microcontroller?

[RayJones]

By the "servo" I presume you mean the model type with a nominal 1.5ms PWM control?
There are many and varied servo systems in the world 

If so, obtaining a PWM signal from another system will not cause an issue, so long as your grounds are commoned.

You could use an opto coupler if you really desire isolation...