Mission Bay comments...
I keep my boat in Mission Bay. Most of the marinas are outside the Mission Bay Drive bridge. However, all the launch ramps are inside the bridge. it sounds like you are going to trailer your boat over from Arizona and you want to launch in Mission Bay. Trailerable boats 26 ft and under should have no problem with that bridge. However, the Ingraham St. bridges are much lower. Use the launch ramp at Dana Landing to avoid having to go under these bridges. All ramps in San Diego are FREE. There is a beautiful 72 hour anchorage in Mariner's cove. Nice place to stay, especially if you have a dinghy.