I'm a technology instructor at a new Applied Tech HS setting up a long term rover project and working out the kinks over the summer. I will ultimately be using the Dagu wild thumper and a sabretooth dual brushed esc. for our projects. 

For now, due to time constraints, I picked up a Dagu Rover 5 and a t rex dual motor controller. I've had success setting the rover 5 up as a straight up RC vehicle using a spektrum dx4c rc car controller and receiver.

Given that success, I now want to introduce the 3DR Pixhawk auto pilot and having a difficult time getting it to work. 

Mission planner reads channel inputs but the T Rex isn't seeing the signals and thus no outputs. The T Rex blinks rapidly green. I was able to calibrate channels in the trex calibrate mode but once I reboot with jumper off it isn't responding.

Regardless of where i place outputs on the pixhawk the only channels I get response on are pitch and roll - I've got the mixing jumper in place and wonder if there is an issue there as Pixhawk would do the mixing? Regardless with or without the mixing jumper, I'm not getting any signal to the trex.

I assume the trex should remain in rc mode? or would this be an analog input?

I'm using a Spektrum system (PWM) and the PPM converter sold by 3DR.

Not clear which channels on the PPM converter correlate to the necessary channels for driving the rover with a surface controller. If easier I can change to a 6 channel air system and use right stick.

Also a bit unclear what servo wires I need from T rex to pixhawk aside from 1 and 2 as it would seem that pixhawk is taking over for sending signals for mode, etc. 

I have a lot of experience with the Pixhawk on multicopters but a bit confused with the rover clearly.

Any help greatly appreciated