do a search on the forum before you drill. Not sure what you plan on putting up there, but the ply's on the roof are the weakest part of the top. Not saying it won't work - people have done it but there are far stronger, less expensive and less intrusive options. Look at Thule gutter racks.
'07 JK 2dr Sahara - auto w/ 4.10's and rear locker. 2" OME HD coil lift, BDS shocks, and 1" body-lift. 34" Hankook RT09 MT's on 16" AEV Bridgers. ARB diff covers, Warn bumpers, Warn 9K winch, a couple Hella lights ...and a WORTHLESS AirRaid CAI.