EQ in the loop can do wonders depending on the tone you're after. I put a Boss GE-7 in mine for a while before I realized the chip in my King of Tone was the problem more than the EQ (reading upstream, I should note that my dirt pedals are now a KOT and a Monsterpiece STUD, and I now use crunch on channel 1 for gain and blues on channel 2 for cleans). Changed back to the stock chip and it was fine.
The real key to dialing in these amps, I've learned in the year and a half since I wrote the above, is to simply dial them in left to right. Literally. Start with the master roughly where you want it, and with all other knobs at 8 or 9 o clock. I like to do this with the reverb and contour off. Then turn the gain up while strumming a chord. When you get that where you like it, go to treble. Then mids. Then bass. Dial them in slow. Turn up, back off a hair, turn up again, etc. After getting bass set, I like to fine tune treble, mids and bass by strumming a D, A and E chord, respectively. The crunch and bite of the treble on the D should sizzle, the mids on the A should punch, and the bass on the E should boom. That last part might just be tuning to my ears, but it works for me. It usually doesn't require much if any tweaking -- it's usually right. When all that is done, set reverb to taste, and then if you like, set contour to taste.
This maximizes the tone stack in a way I haven't been able to duplicate otherwise. You really get the amp dialed in right. I think most people do what I used to do, which is start with everything except master on 5 and tweak from there. The gain stages in the tone stack don't really mesh well together this way, and dialing them in in the order I suggest affects the tone in descending order of impact on the gain stages. So gain affects it the most, treble 2nd most, mids 3rd, bass 4th. It's much better to dial them in one at a time because you get a better idea of what each does to your tone as you go, and it's easier to correct on that one knob than it is to figure out which one goobered up your tone.
I figured all that out by reading the manual, so this isn't some big secret I've uncovered. But I thought I'd share it because it works, and it works very, very well.