I don't have at JK but I love my Trektop NX. I Never take the top completely off. Because 1) it turns in to a safari top ( No sides or corner panels left in place) and 2) skin cancer run in my family. But the windows are fairly easy to take in and out. The most difficult part is getting the corner panels back in place but after doing it a couple times you get the hang of it.
I might be a little but I LOVE my Jeep.