Gotta be very careful about connecting output jacks from amps to soundcards- can blow out your soundcard. Would suggest putting in a little mixer between the amp and the soundcard so you can monitor and control the line-in. Or you can look at using a recording software that supports VST plugins that will allow you to use your computer as an amp modeler/effects processor while recording or for adding afterward. One big advantage that you have when adding the fx after recording a clean signal from the guitar is that you can do massive tweaking to get just the right sound. If you are recording with the fx already going, you are limited in what you can do in the production phase. At this point, I plug in direct from my electric or acoustic/electric into the soundcard and add fx later (hop over to
Radio Shack and get a 1/4" to 1/8" adapter to pop on one end to go into the soundcard if you go this route.
Keep reading the other posts in this part of the forum as well. There are a ton of ways to attack this particular "problem".