Usually a live well pump runs directly off the battery. As to which battery it just depends on which one its hooked to. Normally the starting battery assuming the other 2 are for the TM.
Does your boat have a master on/off switch? That's how my ProCraft is set up. As long as the Master switch is on all accessories are able to run without the motor key being on.
nothing should be connected to the ignition other than necessary items for the motor. all accessories, should run thru a totally different system with fuse block. see wiring diagrams at the top of this forum.
