I've done both and I also would recommend taking them off the first time. Doing this gives you a really good feel for where everything is, and prevents you from stripping the screws.
Put the carb screw kit on that first time. Brent's kit is better than just Home Depot bin hex screws...plus the little washers are a nice and necessary touch. Either way those will definitely help if you want to do it w/o pulling the carbs.
Another thing that helps me is a custom-ground ~2" screwdriver that fits right up into the jet holes. The rejet process takes me less time than the carb balancing, screw setting, etc, now.
Oh one last thing - and others probably have better methods than this - draining the bowls: I just use probably 15" worth of aluminum foil folded up several times in the form of a chute and set one end under the bowl drain and the other over a coffee can that I can place a-way's from the bike.
