I've been reading up about the two head's, and what I'm wondering is what is the difference. In the specs on the Peavey site, the only difference is the JSX has presence and resonance controls - and they look difference. The valves are the same as well, so I"m just wondering what the difference is if anyone knows.

2 different amps. Go test.
Washburn USA Custom Shop
Pretty big differences. The JSX is Joe Satriani's signature amp. Its designed for him. The XXX is just a normal production amp, not anyones sig. The JSX will be better for Joe's tone, as it was built for him. They may have almost all the same spec's listed on the site, but they will sound much different.
Just like a 5150 is a clone of a Soldano SLO, but they sound very different. Except the JSX isnt a clone of the XXX, its more of a refined and tweaked version.
The XXX was a starting point for the JSX. The guys from Peavey modded, tweaked, and changed things according to what Satch suggested and/or asked for. The JSX has better cleans and is slightly more articulate sounding than a XXX.