Hi Lindsay,
I would suggest housing the documents in uniformly sized card stock folders large enough that the largest documents will not protrude from the edges. If the documents are in poor condition (with delicate media or vulnerable tears) they should be stored in individual folders, or if they are robust you could group them, a few per folder. The folders could then be stacked in boxes and stored flat on shelves, or placed in flat file drawers. Labeling folders in graphite reduces the need to paw through the documents to find the particular one you’re looking for. Box and folder material should ideally be acid-free, lignin-free, and buffered, and the documents should not be packed too tightly in boxes or drawers. Since parchment is a very moisture-sensitive material, making the effort to avoid exposing the documents to extremes of humidity during use and storage will help to keep them in stable condition.
I hope this is helpful, and please let me know if I can clarify anything.
Rebecca