If I understand your problem, when you run the bow thruster, your instruments shut down, and the bow thruster stops after a few seconds.
It sounds like the high power draw of the bow thruster (>480 Amps) is pulling down the voltage of the batteries to the point where the instruments shut down. My first guess is that that problem is the batteries are weak.
It will not completely fix the problem, but a help would be to run the generator with all battery chargers whenever you are running the bow thruster.
Fort Lauderdale, FL, USA