I would avoid the use of fuses in the windlass power circuit.
If you use a breaker, and size it right, the breaker will trip on overload and save your windlass motor when you do something stupid one day, like try to haul a stuck anchor up with it and go to locked rotor amps instead. If there is a breaker already at the dash, the breaker at the stern can be higher rated but no higher than the new cable is rated for continuous running amps at the cable temp spec.
Breakers are resetable so you don't have to fumble for a fuse at the worst possible time.
In the case of the motor feed, if you select the right rated breaker, it will protect the windlass from permanenet $$ motor damage. The windlass motor manuf will direct you to the right AWG gauge of the feed based on total length.
If you choose to run a neg feed also, the electronics will see half the voltage drop they would have seen if just going to new positive feed. You can try it out first, since copper power cable is not cheap.
The advice on breakers for motor circuits is universal, when the motor doesn't have built in overload protection, like a motor driven AC compressor have.
Modern electronics are way too sensitive to voltage drops, their power supplies are not sophisticated enough since the vendors are cheapng out to save a buck. Depending upon what you have, windlass wise and electronics wise, the solution you are undertaking may or may not work, if it doesn't work, then connecting the new power feed to starter battery will.
