It seems to me all your tone is coming from the gain since you have the other controls down so low. Try silicon diodes and turn up the mids and master.
I think of knobs in this sequential manner from left to right:
Bass=tightness>boom or thump>muddy sound.
Mids=scooped>liquidy/creamy>clarity>stiff
Treble=dark>focused attack or bite>shrill
Presence=dark/fat>bright and chimey>shrill
Gain=volume>overdrive>crunch>high gain>saturation/compression>liquid>fizz
I also recommend doing this, which is advice I've given to others in the past and is how John Petrucci ocassionally sets his amps:
Set all tone knobs to 12:00. Put Master volume around 10, at the least. Maybe 11 or 12 if you can afford to.
Then turn the gain off to 0, close your eyes, and start chugging your low string. With the other hand bring up the gain slowly to listen to its effect. Go far out into mushyland, then bring it back down all the way. Remember, eyes are closed--you're not looking at where the knob is. Bring the knob back up slowly again and stop when you feel you've gone from volume increase into crunch. Keep going and listen for when you reach fizz and mush. Then bring it back just a bit so the knob is right before this threshold. This is your gain setting.
Now move to the treble knob because this one controls the amount of tone that passes to the other knobs. Do the same thing with closed eyes, off to full, bring it back, etc. Except now you are listening for when your tone goes from blanketed to defined. How much bite, cut, attack, definition, etc. Stop when you get to where it's too bright and thin and too articulate. Then bring it back just a bit and leave it.
Now move to bass. Do the same thing, eyes closed. Except now you're listening for tightness, body, and most especially for muddiness. The tone will get muddier the higher you go up. Be very sensitive with this knob. As before stop when it arrives at mud and then dial it back a bit.
Next comes mids. Rectos are the opposite of Marks--they lack mids. What you want to listen for here is first of all the total spectrum of the mids knob. Eyes closed, do this a few times to get a good feel for the mids. Then go to off and start bringing it up. Listen to the variation between scooped, to undefined, to clarity/definition in the notes, to finally a point where it feels like the string becomes a steel rod and you have a square sounding amp. The mids have a huge effect on the feel of the strings. Very little gives it a liquidy feel. Too much gives it a steel rod feel. Just enough means you can feel the strings under you. Find the spot where you can feel them and where your amp has definition and clarity.
Finally, go to presence. Go left to right as you've done with the others, eyes closed. Presence is going to affect the brightness, and it will fool your mind into affecting the girth/body of the tone. But Presence is only extreme highs, so how does it affect girth? The bass is the one really doing that, right? Well, the Presence controls how much you get to hear the settings of the bass, gain, and Treble knobs. It's like a filter. Too much Presence and you've got a nice defined tone, but it'll slice your ears off. Too little and you've got a blanket on the amp. You've got to think back to the guitarists you like and try to recreate that here. Find the place where you get attack and definition without getting fizz/slicing highs.
At each knob, use your ears, not your eyes, and look for that "moment of change"--when the amp enters yuck territory. When you hit that threshold, click it back left a little and leave it. Each knob needs to be complemented by the others. So if you like really high treble settings, you'll need to balance the tone by bringing up another knob with it. You shouldn't leave any of the knobs down by themselves in my opinion.
These "moments" are different for everyone's tastes. For example, Mark Tremonti likes a full bass knob. I like my bass just below 9 oclock.
