I believe you will need a coprocessor that can give commands to your Flight Controller over MAVLink. That could be one of several types: Raspberry Pi, Arduino, Odroid, full PC, etc. There are examples of how to use MAVLink on these. For instance: MAVLink and Arduino: step by step. But if you search, you will find more examples and documentation on how the protocol works.
I have plans to use a coprocessor on my current lawn mower rover and on future agricultural vehicles but I have not delved into it yet.
Good luck and please keep us posted on how you progress!