Fuses are to protect the wiring, not the device. If you have a short, the fuse pops so you don't turn the wiring into a large heating element. Given that, and ideally speaking, you need the fuse (or breaker) as early on in the configuration as possible. The closer the fuse is to the power source, the more protection it offers.
Now... whether you want to run it directly to the battery with its own fuse at the battery, or run it from your panel is up to you. I guess the biggest deciding factor would be, does your panel supply enough amps to run your trolling motor along with everything else it has to run? If yes then you have a choice. If no, then the choice is made for you.
