-up in here (maybe when inside a room upstairs?)
Yes. I'm up (stairs) in here (in the bedroom).
Saying "I'm in here" doesn't give the impression of 'up', and saying "up here" doesn't mean 'in the room'.
Could anyone please take the mystery out of these three?
When should I use "in here" or "up in here" for instance?
You shouldn't. It would be a grave mistake to think that, just because you've heard some Americans saying something, that you actually have to say it. (Of course, that goes for what Australians and others say as well).
If you want to use it, wait until you are up somewhere and in something.