I have a new Minn Kota Trolling motor, on the 3rd time out the inline fuse holder coming from the positive battery terminal got really hot and melted the holder. First i thought it was due to wire but i moved the motor to the from of the boat and plugged it in and it melted the other wire fuse holder.

You must provide a lot more info for us to provide assistance. What pound thrust motor? What voltage? (probably 12) Do you know the amp rating of the motor? Where did the fuseholder come from, what fuse is being used in it, and what gauge is the wire for the fuseholder? What gauge wire is in the boat harness, and how long is it? How is the TM being connected to power?

My first observation is the fuses in the fuseholders appear to be over-rated for the fuseholder. I say this because all wire has an amperage rating, and the largest fuse that can be safely used in a circuit must be of a rating smaller than what the wire will support. I'm guessing that someone up-sized the fuses in the fuseholders. That doesn't work, as you've discovered. A 30 amp fuse will fit a fuseholder built for 20 amps max based on the wire used for the fuseholder, for instance. That move will allow the system to melt the insulation because the 20 amp fuse is no longer there to protect the wire.

Most trolling motors draw too much amperage for an in-line automotive-style fuseholder (with wire leads) that must be connected to the harness. The heaviest automotive in-line fuse assemblies I've seen support 30 amps. Yep, a lot of trolling motors will melt that like cheese on a cheeseburger.... Answer the questions above and I can tell you what's wrong and how to correct it.