Well there a few ways to do this.

You don't mention your current setup, but if you have an existing soundcard, you can get a mixer and hookup the master outs into the soundcard inputs. Pan the two channels on the mixer hard left and right. This way the signal will be recorded separately.

The other way is to get yourself an Event Layla or MOTU 2408 or some other soundcards with multiple inputs.

Hope this is helpful.