It's been a while since my last post as I have been trying to get the APM to work.
It turns out that JP1 on the APM appears to not power the servo out as stated in the manual. But this is not a problem as I will be using a BEC in-line after the Power Module for the APM.
I have also decided to change the power over to Lipo batteries as I want to drop the weight in the plane.
Also got the remote to change between stabilized and auto flight.