It depends on the vst you're using. Amplitube can have stereo inputs with their own signal paths, separate amps, effects, outputs, etc. You could set up a buss send both guitars panned hard right and left to take advantage of the stereo path. I wouldn't go that route though. I would set up each guitar track(s) separately using their own vst(s), get my sound and freeze them to save cpu cycles.
Rocky