Is it possible to track both paper and online card inventories? Or would that be two seperate accounts?

Deckbox doesn't officially support MTGO. For instance, some of the online-only editions such as Vintage Masters are missing. In addition, there's no support for the Tix currency or trading digital cards.

That said, I personally don't see any issue with creating a separate account to merely track your online inventory, as long as you're fine with the lack of online-only edition support (and don't expect them to be added, cuz I suspect they won't be) and are careful not to mark anything for trade.

I think it's technically against the TOS to have two accounts, but since you're not trying to abuse the system (e.g. completing fake trades to beef up your trade score) and you'll just be using it to privately track your inventory, I doubt it'll ever be an issue. I have a second account that I use simply to test CSV imports or the like.