Yes , you should put the wire in a bras tubing that the wire just fits in. Make the bras tubing as long as possible in the boat and about 3 to 5" on the outside going towards the strut and prop.

Make sure not to bend the bras tubing in any way or your wire will be stuck in the tube and cause drag.

Here in Europe wire drive is being used in 90% of Speed Electric boats for competiton and it works great and cheap.