I'm certainly not alone in using your service not only to hold decks that I currently have, but to build decks that I think are interesting. That being said, I think it would be nice if there was a way to add a check box indicating that "Deck X" is currently active and as such, the cards will not show in your inventory for purposes of building another deck.
For instance, I have a budget-ish Mono Black deck which uses Rakdos Shred-Freak in it: http://i.imgur.com/qpEHaCY.png
As you can see, I have four in my inventory and they're all used in this deck. However because I saw a deck that looked interesting, I imported it: http://i.imgur.com/2lBDObC.png and as you can see, it essentially wants me to take my cards from my black deck and put them in this deck.
What I would like is if I could mark my black deck as active so that when I went to the other deck, it would show [perhaps even in another column or something] that I would need to buy these cards if I wanted to make this deck while maintaining my other deck. Also, this would be beneficial to people -like myself- who share a library with their significant other, who also plays and builds decks.