Have a sump for the drain with a small
pump. the sump would be separate from the rest of your bilge. Maybe a tupperware tub
(they come in various sizes and shapes) could be used for the sump or something similar. And then your bilge will be not be wetted by the A/C drain... and if the bilge is still flooding then look for other problems.
The sump's nautical term is a Rose Box.