I leave the bar on, admittedly I'll get a few scratches. That way the soft top will match the paint chipping off the door hinges.:toung:

 

Which way do you roll the side windows? They don't seem to roll real well and quite bulkly when rolled - I've been leaving them flat in the back with a towel between. But that takes up my cargo space.

 

I roll the back window up with the bar in it. I too have some scratches, but I don't think it is from this.

For the side windows, I have an oversized beach towel that lay between the two windows and around the other side of one. I then roll the windows into a sort of tight cone shape, keeping the plastic track and the window J channel straight. Once rolled up, the towel is exposed on the outer side. A couple of extra Velcro straps secure the assembly and I CAREFULLY slide the whole package under the rear seat. Works like a charm!