Yes,raising your bottom bunks will cause you to have to back down the ramp further to launch.It will not affect the towing at all.Do you have room to space the fenders out away from the trailer frame and boat?You only need an inch of clearance between the fender and the side of the tire.Do you have side bunks or guide ons(AKA goal posts) on your trailer?You maybe able to move those in a little to keep the boat from shifting on the trailer.Pics of your set up may bring in some other ideas.