Truefire has a post featuring some helpful tips for recording your guitar with a digital audio workstation. The article is written by Rich Tozzoli who has apparently done a fair amount of work creating the audio for commercials. Here is an excerpt:

"7. Split 'em up
One great way to get maximum flexibility on your recorded tracks is to split the guitar’s signal on the way into the DAW. Using a splitter, or even a pedal with two outputs, you can run one clean signal directly into the computer and one to an amp for miking. Send the signals to separate tracks. Once the two tracks are in the can, you can add a processor/plug-in on the clean channel and blend it with your amp sound for a thicker, nastier tone. And what could be better than that?"