Bestop's is pretty easy to install and remove... I'm sure other companies are very similar for the jk. No drilling or modifying nowadays.
I actually keep my header channel rolled up in the bikini top when not in use.
2010 2dr Wrangler
2.5" ProComp Lift, Front Adj Trackbar, JKS Disco's
Tera Front Lower Controls Arms, Rear Upper Control Arms, Synergy HD Balljoints
Tom Woods 1310 Driveshafts
33" KM2's on ProComp 7069 16x8's
AEV Premium Front Bumper, IPF 900XSD Lights, Warn 9.5ti w/ Synthetic Line
AEV Rear Bumper, Tuffy Security Deck
D30 Front Sleeved and Gusseted, RCV's, ARB Locked
4.88 G2 Gears
D44 Rear ARB Locked, Chromoly Shafts