Oh! I see your problem! Yeah! You do it by dragging and dropping.
Right now, when there's stuff in it, if you just click on the box or use your enter key, it skips right to the "How man you want dialog", right? That's for speed, so you can just run through your pantry and pick stuff up in a quick way. But, if you want to put something in your inventory into a box that's got stuff in it, you just gotta drag it from your inventory to the box! It works pretty well that way.
Anyone know if in the future, with Furniture Making II, if we will be able to make our own SDBs? Now that I'm using them, of course now I want more. :)
I like how, even if you have multiple stacks of an item (on your person) to add to an already populated SDB, you don't have to drag. each. stack. separately. to it. It's just one drag and go. Very nice time saver.