You could do it any way you wanted, I'm not sure what's confusing about it. Ideally you would have a bankroll that you didn't touch, and your winnings would go to that. It could be in your bank account, you would just have to keep books on what was "poker money" and what wasn't.

If you're a pro, you would assume all or almost all of your wealth would be game for the poker table.

I don't see how it's different from online.