Think about it in terms of objects.
If your binary tree is building “rooms” you can store whatever data you want about a particular “room” when it gets generated and placed in the tree.
Think about the structure of a binary tree, or at least research it a bit, the links provided in a post above are quite useful.
The leafs of the tree at the bottom of the structure will be your final iteration on the tree, thus the final “version” of the generated dungeon. If you use objects to represent your rooms, upon generation you can store perhaps the width and height of the room within the object thats held in the tree.