hi there; long time lurker, first time poster... anyway:
Amplitube has an awful lot of variables to select through, and in my experience presets have to be tailored for a particular guitar; some of my presets sound great on one of my guitars, but really terrible on another. Try to set it up from scratch, if possible, and use the EQ's, both amp and post. Every heavy amplitube preset I've ever heard has had too much Mids in it, at least for my guitar. Experimentation is key.
Having said that, there is a trick that I've been guilty of using in the past that could be considered "cheating", but we all get lazy sometimes. Find a song with a guitar sound that you really like in it, and find a part that's at least a few seconds long where there's just guitar- no bass, drums, or vox. This can be hard sometimes, so dig through your CD library. Get a WAV file of just this part and save it somewhere. Now, in Amplitube, try to match up your guitar sound to that WAV as best you can, which won't be that close since, let's face it, Amplitube is a neat effect but not a guitar amplifier. Next, download the demo of
Voxengo's CurveEQ and insert that after Amplitube. What you'll do is load up the WAV of the guitar sound you want into Curve EQ and match the frequency response to that of your guitar sound. Curve EQ shows you a frequency response graph- take a screencap of this, or write down where you need to cut and boost and by how much (you need to get a screengrab or write it down because the CurveEQ demo inserts silence every few seconds). Then get rid of CurveEQ, load up your favorite EQ plugin, and imitate the frequency response you just wrote down. Obviously you'll need to tweak it some, but this method at least suggests where your frequency problems lie.
I imagine this method would completely horrify any seasoned studio pro

, and clearly it has problems considering that most guitar sounds are comprised of two or more different guitars and amps, but if you're totally stuck and can't get a decent sound, it can serve as a guideline. Unorthodox, yes, but using a program as an amplifier requires unorthodox methods.