I made some bags for a few of the decoys I have made. I just sewed a peice of canvas into a tube and then sewed closed one end. The individual decoys get put into these bags then into a normal decoy bag.
At Walmart for ten bucks, you can buy the shoe organizers. They come in brown already and they have stiff padding between each slot, but it collapses down when empty.. So its win/win. They will hold just about any duck decoy... Probably not geese lol. This isn't the one I have, but you get the point