Properly controlling a 6V servo motor from a microcontroller?
So in general when you have a noisy actuator and a sensitive you run them on separate supplies and try and keep the two electrically isolated.  I use a circuit like this when I try and opto-isolate a transmitter and a receiver:

This will give you a non-inverted output of the input waveform, and will actually work with any voltage on the input and output side so long as you can still turn on the LED (i.e. the input voltage is high enough) and you are within the operating voltage of the output transistor.

Isolating the two supplies is actually good in a lot of ways.  It means you don't have to worry about surges in current on the actuator supply causing issues on the microcontroller (fewer decoupling caps, etc), and it also means that if the actuator battery dies, the actuator won't try and run off the input signal from the microcontroller.

Hope that helps!