Once the soft top is down, I roll up the rear and stick it underneath the top, then tuck the side windows between the top and the back of the rear seat...works perfect, windows don't have any scratches and I've had it for 2 years like this...
Also if you get scratches, get the Novus plastic cleaner system, it works wonders, makes the plastic windows look brand new

 

Looks good man.

 

Looks GREAT!
Your JK is my favorite one on this site. Would love to see some photos with the top and doors off.

 

I went to local fabric store and found grey fleece, my interior is grey, that just happened to be on sale. I think I got 3 yds. Just lay it out, put one window in, fold fleece over, put another window in, fold more fleece over, put last window in, fold rest of fleece over, roll it up. Everything stays nice nice, except for the large amount of dog hair the fleece attracts

 

Many thanks for the tips on the windows, you guys.
Rolling them up in fleece and then putting them in a tubular bag seems like the best option.

Got the top's first rain tonight.
I had checked it with the power washer after installation but very heavy rain for a bit tonight and no leaks at all, even on the interstate at 75mph!

Now it is a '09 top I got from Tango, don't know if any improvements have been made but the header bar is very tight and secure, someone said they were going to make it stiffer. Don't know if that's true or not, but I'm very pleased to say the least.

Also pleasing is how quiet it is. The hard top is quieter, but not by much. I'm not selling my hardtop, but it will see less running time down here where there isn't much severe winter weather. Since I've added the Tuffy console insert and glove box, I'm not too leary about leaving something valuable in the Jeep with the soft top.
My CO2 tank will have the mount padlocked shut, and my recovery gear bag will be cable locked to the roll bar and also padlocked shut.

Any other suggestions would be welcome.