Bestop Soft Top Protectant Kit. It does wonders on my top.
It has a cleaner and restorer for the fabric. And even a cleaner for the windows (though they are a PITA).
Hose the roof off first, then use the cleaner, followed by the protectant every few washes. Actually gives a little color back I think.
Then just wash the rest of your Jeep as normal.
That way you can clean any spots where you get the goop on the paint. It doesn't hurt the paint. But then you just have to clean that spot again...
You can get it just about anywhere. And even the individual bottles.
Here is a link to Amazon though.
Bestop 11205-00 Small Cleaner and Protectant Pack : Amazon.com : Automotive