I think you need to have the amp how you want it to sound (i.e cranked), then compensate the levels in your recording software, or mixer if you ever deside to get one, in the software will be a recording/input fader.
Play something at the loadest part of the song/riff ect and adjust the recording level so that it hits about 75-80% (thats the level i go for, i might be slightley wrong on those numbers though...?) this will give you a good strong signal, without clipping and some 'headroom'
Thats it i reckon.....