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Kayaken it doesn't matter if the boat is upside down. Again why would you want to put a anti fouling paint on a boat that doesn't need it. Is you current gel coat damaged? Barrier coating is just an expensive primer. If your gel coat is in good shape and you still want to apply bottom paint you must first de-wax the bottom and then scruff it up for the bottom paint to adhere.
You can always follow the instructions on the bottom paint can.
But like I said B-4 I think it is a waste of time and money for a trailered boat.
Use the elbow grease to buff a mirror finish on it, which will also help keeping growth off.
Good luck with your project.