Try using a noise reduction plug when using Amplitube or any other VST amp modeller, in case u haven't tried it. I'll explain it with reference to Waves X-noise plug but the process should be similar for any alternative plugs.
Record your guitar track as normal, making sure your input levels are satisfactory.
Now open the .wav and fire up X-Noise. Click the 'Learn Profile' button and then play the initial portion of ur recording (before anything is played). Stop playback and disable the learn. The plug now has the profile for the non-musical content of ur recording, this works better if u haven't palm muted prior to ur first note. Preview the effects of the plug using the 'Difference' button. Adjust the threshold and reduction until u can hear just the noise, u might need to crank ur monitor level up for this part. Don't be tempted to reduce too much of the signal as it can kill some important harmonics.
Havin applied the plug, try playing back thru amplitube...should be a helluva lot cleaner.
You can record the noise seperately by hitting record and not playing anything, but I prefer to use the beginning of the recording. This way the noise profile will be more accurate for that take, ur exact sitting positions, levels, etc.
Even if u think your overall sound is clean enough through amplitube, try using a little noise reduction on the raw .wav and the sound becomes a whole lot cleaner.
Hope this helps.
