I have a 40 pound thrust trolling motor it mounts on the transom But the battery is in the front of my boat I have a 16 foot jon boat the plug outlet for the trolling motor if also in the front of the boat I would like to run 6 gauge wire to the plug any suggestions would be appreciated Thanks.

Are you gonna just be running the trolling motor off that battery, or something else as well?  What says you cannot put the battery in the back?  If you move the battery to the stern, and you have enough length on the TM lead, just change the end to ring terminals, and attach to wing nuts on battery.  If the leads are not long enough put a plug on it, and run 6 gauge wire from the battery to the plug.

If the battery has to stay in the bow, forgo the plug you have completely.  Now, run 4 gauge directly from the battery to the plug on the trolling motor lead.  Make sure the plug is suitable for 4 gauge, or it will be a limiting factor, and you will lose power.

Oh, and put a 40 amp fuse somewhere between the two.

or a circuit breaker (about 1 ft from battery)

The circuit breaker costs a bit more but is "reset-able".  Stinger electronics makes some good ones for 12v.

Not sure if you have Prince Auto in the U.S. but I seen circut breakers for $5 last week.

Garnet