The air should be able to run underway without issue. The number one thing to watch with air conditioners is proper waterflow out of the exhaust and make sure the units aren't icing up after periods of run time. Air pumps are not self priming and can be problematic until you get a good system in place to prime when the boat comes in or out of the water. First thing I would do is hook to shore power and run the air unit. It takes a minute or two for the pump to kick on but make sure you have water coming in and leaving the boat. If you do, this isn't your issue. As mentioned in a private email, I would pull the manual to the air unit and see what's E1 represents. If it says anything about temperature or freon chances are you need to make sure you are first pumping water.