Hi Photo-Dude, I have done the same thing with my 29.5 Hunter, now is a lesson learned, before you take the boat out of the water you must close the seacock that is located next to the strainer or you will drain completely the line and the pump would not work. Now your problem is that the pump used for the marine AC is a pump that would not start unless the line is full of water, having just water in the inlet side would not be enough, you must have the whole line full of water. You cannot have any air in the line. I will tell you how to cheat the system, get a piece of a small hose that will go into the outlet on the side of your boat, where the water normally comes out of the boat, and attached a water hose to it, open the water a little bit and with the seacock open let water into the system. If you watch on the side of the boat where the seacock is you will see bubbles of air coming out as the water keeps pouring in from the outlet few inches above the water line. When the system is full there wont be any more bubbles of air coming out and water will be coming out of the side of the boat, pull the small water hose out of the outlet and now your system is full of water, start your AC and the pump will start pumping water.
Another way would be to close the seacock, remove the hose from the outlet side of the pump, use a smaller piece of hose 3 or 4 feet long, enough for the other end of the hose to be above the outlet on the side of the boat and with a water hose start injecting water into the system to fill it up with water, when water is coming out of side of the boat open the seacock and water will start coming through the pump and into the bilge, rapidly take the smaller piece of hose from the line and quickly insert the line into the pump outlet, tight the hose with two clamps and now your system will be very much full of water with the exception of the little water you lost during your connecting maneuver but you wont have an air bubble in the line and you will be ready to start the AC. This is not the prefer method because the hoses will be very hard to pull from the pump and just as hard to push the hose back into place specially since there is not much room to bend the hoses . If you use the heat of a hair dryer you can softened the hose ahead of time so it would be easy to make up the connections. Maybe someone has an easier method and he/she can share it, otherwise this is how to do it. Hope this helps you to remember to close the seacock next time, I know I will remember. Enjoy your new boat.