I had a similar issue with the boxes. I used to keep them as they were and put small boxes inside the large(r) ones, but they tend to "consume" too much space. Eventually I flatten them out and had an extraordinary space reduction. I don't think the flatten boxes would be useful if selling parts of the collection, but I don't have the hart to dispose them. Besides, I like having some large pictures of the sets that exists in the box cover. On the other hand, I don't keep any DS (plastic) bags.