hmm, wrong forum for this...
anyway, yeah, knowing what software you're using would help. but see the great thing about using stuff like amplitube or guitar rig is that it records your guitar clean. you WANT it to do that. that way you can always go back and re-amp the original clean signal anytime you want or need to.
whatever program you're using, there should be a way to apply the effect to the dry track. in cubase you click on audio - plug ins - (desired effect). then from there you can pick which sound you want, preview and tweak it to your satisfaction before applying it.