The setup for an a/c system is normally thru-hull ->strainer->centrifugal pump->a/c unit->overboard. If you tee into that system, say immediately after the strainer, there is a possibility that the lift pump for the watermaker may suck air backwards through the a/c pipework and push it into the hi-pressure pump. If that turned out to be the case, an either/or selector valve would solve the problem.
If all else fails, read the instructions
If it ain't broke, don't fix it