I have a Tree of life box for my Morgan Greer deck, but I keep it in it's box within the box if that makes sense?
For my Universal Waite, I have it in a lovely little box that I got from the dollar store.
For The Robin wood, it's in a greenman box that a friend had painted for me and it just goes with the greenish pagan theme.
For my Greenman Tree oracle, I don't have a home for it, it's in it's original box until I find one that suits it or make or obtain a bag for it.
For my Mythic Tarot and Tarot of the Renaissance, they are still in their original boxes and I'm not sure where their new box or bag will be. If something jumps out at me, I get it. Lately I've noticed I've got a box that kind of suits it's personality. Of all the boxes so far the Tree of life box (That I got from The Witch Shop of Pa online) and the Greenman box that my friend Ilanah painted for me are the most special.
But to answer the question (sorry, got wordy there) I keep them in the box within the box. I don't know why. I suspect if I have a bag big enough, I'd keep the box in the bag. Maybe one day I'll get brave and let them out and stay in their places without the other box. I think it's self-preservation because one of my kids spilled something on my box and I quickly rescued it and thankfully, the box protected my Robin Wood deck.
Interesting....I look forward to reading what you all do.