Hello, welcome to JustAnswer.
If you want to keep the battery for the motor isolated you are going to have to add two new 12 volt batteries and run them in series to the new trolling motor.
Then, in order to run the other accessories off of one of the two new batteries, their power supply needs to be isolated to one of the new batteries. So the power and ground wire for the accessories would hook to the same battery while the power wire for the trolling motor would be hooked to the positive of one battery and the ground wire would be hooked to the negative post of the other battery. Then, you need to hook the positive side of the battery with the negative trolling motor attached to it, to the negative side of the battery with the positive wire of the trolling motor attached to it.
The power and ground wires for the accessories that are connected to one oft new batteries MUST be completely disconnected from the motor battery system. Right now they likely share a common ground inside the harness. That has to be removed. So where the ground wire leaves the harness to go into the pump, live well, lights, and fish finder you will need to cut the ground wire, attach a new one, and run it up to the new grounding buss under the dash. The power wires will then need to be removed from the fuse panel they are now attached to and hooked to the new fuse panel.
The positive wire from the new battery is then hooked to the new fuse panel and the negative wire is hooked to the new ground buss bar.
If I am unclear on any point here, or you just need clarification, please ask me, ok? Just post it thru this question and no further charges are involved.