Ok, that is pretty much the same things that I have. Like anything there's more than one way to skin a cat: first I'll tell you how I did my old boat- thoroughly a redneck engineering job.....but cheap and effective.
1) I wired the trolling motor independent of everything else (I'm doing the same thing on this mod) ran the + wire from battery to circuit breaker and then connected + side of trolling motor to the aux end of circuit breaker. Connected neutral from trolling motor to a wire than was directly connected to - terminal of battery. Housed the connections and circuit breaker in junction box from Lowe's.
2) all the other stuff was on 1 circuit. Again I housed the connections in a junction box from Lowe's. All the components I used were just the same that you would use in your house and then I connected the accessories to the circuit with a heavy duty outdoor extension cord. I used the + and neutral wires in the extension cord as independent + wires ( I could power 2 accessories with 1 run of cord) then I used the ground wire in the extension cord as a common neutral. For example I had a nav light and a fish finder at the front of the boat. I ran the extension cord up to the front and connected black wire in extension cord to + in nav light, white wire to + in fish finder and the neutrals from both accessories were connected to the green wire. Back at my switch panel/connection box the neutral was tied into a common neutral bus and the + for nav light went to switch + for fish finder was connected directly to main circuit.
In a nutshell, everything was run off one circuit and all the switches were on the + side of the circuit.
It wasn't very pretty but it was cheap(er) and worked fine.