I run S/PDIF out my amp (Vetta II) With a dry signal.
The only thing being recorded is the dry guitar signal. I can then re-amp.
Send the recorded guitar back out to the amp. I find this works great getting just the right tone and EQ settings to get the trac to fit in the mix. Its a lot less work and I can always change my tone at anytime.
I am starting to record everything in this way.