Just use a good mix of car wash and clean water. Forget about trying to avoid scratches on the windows. No matter what I have tried it seems to just happen. I am sure that you could buy some type of scratch remover but just replace it if it gets too bad.
Mopar makes a window/back window protective bag that uses separate compartments (like a drum cymbal bag with dividers between each). Again, dirt and dust will collect no matter what so just be sensible where and how you store the side and back windows.
Now for treating the bird crap that is a part of nature, if you get a stain try a convertible top cleaning solution. I used some of that stuff back when my old convertible got egged by a bunch of punk kids. Took out all of the discoloration left over by the acid in the egg yoke.
Make sure you coat the zippers with beeswax to keep hard rain from seeping in and clean the drip rails on all rubber seals from time to time. DO NOT USE ARMAROL!!! Its has alcohol and will dry out the fabric eventually causing cracking.
That's about it! - Sean OCD about his Jeep.