I'd experiment with combining different distortions. I use the overdrive on my Fender Ultimate Chorus in conjunction with a Boss Metal Zone, gain about halfway on both, scoop out the mids, crank the bass and boom, its cookin'. Using the distortion on almost any amp by itself isnt going to sound spectacular. The greats always combine the amp overdrive with an external box for variety and a unique tone.

Petrucci's rig has changed frequently over the years, check out his site for the current gear. I know on the 6DOIT tour, he used a Fulltone overdrive box in front of a Mesa Boogie Mark II C+ head. Currently I think he's using Boogie Dual Rectifiers, I don't know what external box though.