don't worry, that's how my setup using a Midi sport 2x2 works anyway.
I think the crucial thing to remember is that your Virus and controller goes into the PC and gets re-routed from there. Like you, I thought that you plug the controller directly into the virus, it would makes sense wouldn't it?
What you're doing is feeding all your modules and gear into the PC and all the various output / input routings are selected by you in your sequencer or Soundiver.
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