One solution is to put the book into the series you plan on reading it with. So if a book belongs to two series, put it in with the series you will be reading this book.
If you don't have a device that Calibre can manage collections, use the Tags column and put in the series order number for the second series. Or if you do have a device that Calibre can manage collections for such as a Kobo or Sony, put in the Series column the series you plan to read the book and in the Tags column, put in the second series. You won't be able to put in the order number, but at least you won't need to add another column that's little used.
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