If you are going to mount the spare tire on the side near the tongue, check the tow vehicle bumper clearance as some trailers will hit the bumper. Because it is below the drivers line of sight you can not see when they are about to make contact. Also make sure it is not going to get in the way of the boat being loaded a little crooked.
Might want to throw a set of these on while you are at it.
http://www.dhmtrailers.com/online/home.php?cat=161 Nothing wrong with welding on the trailer, then painting it. Definitely the cleanest way to mount the spare, and having it mounted under will help prevent theft, by making it harder to access, along with keeping it out of your way. Theft of spare tires is actually pretty common.