If you have a cover that snaps over the bow and cockpit areas you will likely need to have it modified for the mouting points of the tower. If you have a full cover then it depends on the tower and your cover.
Many towers (like our Monster Tower - shameless self promotion) are designed to fit under the standard factory boat cover. Some towers may be toughter to get under the cover becuase they still sit up pretty far when folded.
Check out http://www.worldwakeboardcouncil.com/links.html
for a pretty complete list of companies that build towers, and search these board for comments as well. There are a lot of great towers out there you'll definately find one that fits your needs.
Below is a pic of a tower folding to go under a factory cover. www.MonsterTower.com