I have had similar problems in the past with my bugs. What I did with one of my bugs was that, after I had covered all the rust with body-filla, and grinded every rust patch away. I then went around the whole car, marking the "lowest point" on "water catchment spots" in each body panel eg. panel between the tailpipes, rear fenders(2 holes each), front fender( 2 holes each), etc. All in all I had about 12 points. Even better: On a hot day, hose your car done for at least 5 mins. Make sur it's on a PERFECTLY FLAT surface! Leave for exactly 5 mins, then inspect your car for water drops! Observe on the bottom edges, in and around the wheel, etc. Leave again for 5 more mins, redo your observation.
The last remaining water drops will accurately id "high water catchment" spots. These are the spots where you need to drill ting holes in to allow water to escape more freely.
I then took a 3mm drill bit, and made tiny holes, where I had marked.
I placed my car on jack stands, because MUST NOT be visible when the car is standing on it's own. They MUST be directly FACING THE GROUND!
I then proceeded with the applying of the 1st coat, 2nd coat, etc! I have had no problems thus far, and it drains very well. What's even better is that no one knows my car is full of holes, but I know why I did them!