Wiring boats seems to be a real hot topic both here and on other forums. I see a lot of threads on the type and use of various wire. After trial and error I have found the best thing is to break down and use marine wire. Anyone that is going to wire up any kind of boat owes it to themselves to check out websites like genuinedealz.com. They have good voltage drop tables and good prices on wiring supplies. They ship quick too. I am not affiliated with them, just a satisfied customer.
As far as the wire goes, your standard wire that Lowes etc. sells will be THHN. It has good electrical characteristics but is stiff and if it is used in any saltwater application can corrode faster than the tinned marine wire. The marine tinned wire generally has more individual conductors and is very flexible. In addition the insulation is very moisture and oil resistant. Compare a cheap piece of nylon rope with a good piece of braided nylon and you will appreciate the difference.
I really like the connectors that Captain Ahab talked about, the one from Grainger. They make the connection from your #6 to the #8 or#10 trolling motor wiring pretty **** easy.One more thing, bring out the wallet and buy the correct fuse or breaker.