I'm not a blues master or anything, but I've spent some time working on this issue myself. For me, I use as my model the sound of a pushed Fender blackface type amp. I've got a 65 deluxe reverb re-issue, so that's what I'm talking about.
For me, to get a decent blues tone on a Mark series amp, you've got to start with a decent clean tone (ie, channel 1). Even if you don't want to play it clean, you've got to start there. If you've got an open-back combo, I think that you've got to do Vol 1 on 3-6, Treble on 6 or so, mids on 6 or 7, bass on 3 (humbuckers) or 6 (single coil) and do the PULL SHIFT on the bass. This is key. Give it enough master volume so that it's got some punch. If you're using humbuckers and are running Vol1 closer to 6 than 3, try the pull bright. Yeah. That's a clean tone. Play with the presence as necessary.
Once you've got the clean tone dialed in, copy the settings over to the lead channel. Again, do the pull-shift on the bass...this is so key to getting an overdrive Fender tone. Dial the Lead Drive only to 3 or so. Don't have the gain too high or the pull-shift on the bass makes it mushy. Also, do NOT do the pull shift on the treble knob. It'll never sound like a pushed Fender this way. As before, dial the presence to taste. Oh, man. you gotta turn off the graphic EQ...we're going for a natural sound here and the graphic EQ is not a natural sound.
So, with this kind of approach, you should be getting some nice and natural overdrive...not too much saturation...not too much boogie metal sound...just nice somewhat overdriven guitar. No Santana, no metallica, just real. For me, with my amp, this is yummy.
Good luck.
Chip