Hi @hjz_123,
“ArduSub Companion Software” is the full name of the old software we used to run on the Onboard Computer, before BlueOS was released. The old Companion software only works on the Raspberry Pi 3, so BlueOS is your main option here.
BlueOS is intended to be portable to different platforms, but it’s currently not tested on any Jetson devices so there may be changes needed to the installation scripts for it to work. This thread may provide a useful starting point.
The firmware running on your flight controller board (e.g. Pixhawk) is largely unrelated to what’s on your Onboard Computer (as long as they can talk to each other), but given you’re using a BlueROV2 you presumably want to be running ArduSub (which is likely already installed, and can be updated from the BlueOS web interface).