Payload management from Ground Station

Hi, I am new in the field of autonomous vehicles and I would like to ask for advice.
I have to build an autonomous boat that has to carry a scientific payload with different sensors.
I would like to use a board with ardurover, such as a pixhawk, and a companion computer for payload management (Maybe a raspberry).
The boat must be totally autonomous, both in driving and in the use of the payload.
I would like to be able to upload the mission and receive telemetry from a Ground Control Station.
There is a way to take advantage of Mission planner/APM planner 2 to upload a mission that not only includes the waypoint location but also the informaton of which specific payloads activate or deactivate at any waypoint?
maybe using relay pins? Or should I modify CGS software?

The normal way to do this is have the companion computer receive the mavlink telemetry data stream. It can then process it and take any action it needs at any time.

There are commands to operate ArduPilot relay’s etc once you reach a certain stage of the mission. If the operation of the equipment is relatively simply it should be possible.

Thanks, Grant.