Bait boat pixhawk setup

Hi. I have a twin motor bait boat. The motors are controlled from the right stick of my flysky FS-I6x with mixers, running fine. I have added a pixhawk and everything looks to be working. I have looked online and followed how to’s and when it gets to the part in “servo output” and change the function on the corresponding motor channels I can no longer control the motors. I have channel 8 setup on a two channel switch to go from “manual” to “auto” but flicking this doesn’t do anything and I still cannot control the motors. Any help would be much appreciated, thanks in advance.

What type of ESC’s / motor controllers are you using?

twin motor bait boat - sounds like skid steering.
If you are using mission planner connected via USB - you can watch the servo outputs based on your rc inputs.
Go look up configuring skid steer. All the mixing for the servos happens on the flight controller, not the RC controller. Using Manual mode should allow you to drive the two motors, once you get there, the auto modes start working.

Sounds also like you have to get past the failsafes, arming and a few other things. Persevere - its worth it.

Thank you for you suggestions will be having another go at it the weekend. Will let you know how I get on.