Originally Posted by gpelpel
For best alignment you are supposed to first loosen #5 and #6, then grip the brake levers as much as you can and tighten #5 and #6 while still gripping the levers. This obviously assume the rotors are straight. If a rotor has a bend try straightening it as suggested above or probably better replace it.
if you do that on a BB7, you'll end up with the rotor pressed against one of the pads. that method works pretty well for hydraulic brakes most of the time however, the easiest way for me to do it is to just do it by eyeballing it. put the inboard pad closer to the rotor than the outboard pad and you'll be golden. once you get the hang of it, it's very easy to get the pads parallel to the rotor.
as for bolts #1, and #2, don't touch them, they are tamper-proofed for a reason.
the cheater way to align the caliper to the rotor on the BB7 is to just use the two red dials and move the pads to where you want them in relation to the rotor.