I was hoping that one of our data mavens would come to the rescue, but since they are apparently all trapped under something heavy, my suggestion, for now, is to just snap the hell out of everything. Upload all the photos of the individual boxes to the main product record, but don't make part records for them (I believe current shmax.com policy considers them to be part of the packaging).
Because the small box is sold individually, I would probably handle the small box and large box as separate "products", but mention in the comments for both records that one was sold with the other. At some point down the line we may work out some more graceful system for representing products that are so tightly linked. And, just to be safe, do a photo of both boxes together and upload it to both records, again with a caption explaining the dealio.