I have the 90watt mark V but most settings will be similar. Just remember with a boogie everything is driven from one gain stage to the next so don't details it like most amps. You will most likely end up with most of your eq and gain knobs nearer the center than the extremes. My personal preference for lead is the markIV amp with the bright on and I use the parametric eq. Be careful with the gain and bass settings they are very touchy and can Mudd things up if you go too far. The mark is also very sensitive to pick attack so you may think you don't have enough gain until you pick harder and then wham it hits you in the face. Honestly I looked up John petrucci settings on mesas page and they are Avery good starting point.
Thanks for the shot Muad. Just out of curiousity, what kind of speaker cable do you use 7? I'm a noob when it comes to guitar head/cabs. I always owned a combo. Also, do you plug into the 8ohm jack if you are running 2x12s? sorry for the noob questions.. lol