Agree that you definitely need to keep at least a couple of gallons in your black tank, and I go ahead and add the chemicals at that time. If it sits for very long before the next trip, I'll add more chemicals.
Since these critters were flying around, I'd be inclined to not only use some sort of spray down the toilet but to also set off 1 fogger inside. Those little stinkers can lay a zillion eggs and this should take care of both the ones that are alive, but kill the eggs as well. Remember to wash all surfaces that you have food around....actually wouldn't hurt to just give everything a quick wipe off with something like Mr. Clean with Febreeze....something great smelling.