The AC on our rig has a seal that the unit sits on. That is what is suppose to keep the water out.
If you take the inner plastic ring off you will be able to see the 4 bolts and nuts that hold the AC onto the roof. Sometimes these either come loose or they are not snugged up properly to begin with. Reach up there and see if you can tighten the nuts with your fingers. That will be a starter. If they are some what loose you can snug them up a little using a wrench.
Just don't give them to much!!!! The way I remember it---it's just a foam strip used for a gasket/seal, and you don't want to squash it to much.
I would think if that is where the water came from, it would probably be wet up in your ceiling also.
2008 Cruiser CF26RK
2013 Ford Eco-Boost
Heavy duty payload - Max tow