I was worried about that when I bought it but I have had no issues. its a tight fit to install the hardware between th top and the roll bars but its possible. Again the 4 door may be different.
I have a 2 door so this may be different but I put the spiderweb shade on with the hardtop in place and leave it on all the time. Same as the Wrangler I take the bungies of and on to put the front panels back.