Bestop makes the Jeep soft tops, and this stuff to clean em:
Bestop Soft Top Cleaner and Protectant - Quadratec
I use Aerospace 303. I scrub it lightly into my soft top in Fall, before I put the top on for the winter, with a soft bristle brush, then wipe off any excess with a rag. The 303 is awesome on plastic fenders, interior plastics, as well. You can get it from most marine supply stores, some hardware stores, or on Amazon.
Simple Green will work; probably plenty of other options...
If my soft top gets muddy while it's on my Jeep, I usually just go to the coin-operated carwash and nail it with a jet of H2O. You'll find out where (or if) you have leaks that way, as well.