It depends on the track. While I'm writing I'll usually just run the seperate midi channels into the virus and run the audio in via USB if I'm only using it for a track or two. If I end up pushing the poly, then I'll bounce what I need to an audio track. It also depends on what, if any, effects I want to apply to a track.
Once I'm done writing, ready to lay down the final tracks and start mixing, then I'll plug in via the physical outs and record each track manually through my outboard gear. You just have to find what works for you.
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