Ok bounce is one of those terms that I guess means different things to different people. For purposes of this thread, when I say bouncing a track I simply mean making an audio sample out of the MIDI track data. So yes, audio tracks are for samples... your MIDI data of notes and automation stays in one place, the audio output is on a different track entirely. This is something you're not used to doing if you have only worked with soft-synths, and because of the TI aspect of the Virus it's not completely necessary but it solves a lot of problems. But if you do anything with hardware synths (most of which won't have TI or USB streaming at all) or external instruments/voice of any kind it's just necessary.
Working with hardware definitely impacts your workflow so yes you may have some teething pains on your first hardware synth, but at some point you get everything set up the way you want it and you create some templates. Also you're learning a new DAW along the way so allow yourself time to adjust. I think you're not really as far away from getting the stuff figured out as you might think, sometimes you just take a break from it and come back to it when well rested or whatever and you see something you didn't see before.
The part about Cubase that I think you're still yet to arrive at is the notion of buses. At some point you will need to say "ok this output from synth, mic, electric guitar or whatever goes into input X on my audio interface. How do I capture that input into an audio track?" and in Cubase the answer is you must first create a bus and name it something you'll recognize, then you say that bus is the input for that audio track.
Check out this tutorial, it's an antiquated version of Cubase and Windows but the basics still apply.
https://www.youtube.com/watch?v=0-YB-0pC1RE
Now, whatever you create in that process you will have as an option on the input for your audio tracks.
Pain in the ass alert -- Cubase won't let you save these fucking named bus configurations! Well it sort of does, you make templates. What I do is create one monster template that has 95% of everything I'm likely to use in a project, then I make smaller templates from that one that are subsets of the monster template for when I don't need everything. Trust me when I say templates will be important to you, you don't want to map those busses every time you start a new project. Most Virus users create templates in FLStudio for a similar reason, you don't want to manually set all that stuff up every time.