So, I give my box sets their own series page, not numbered, and put my one-offs in there too. It helps that they are all part of the same universe. It's not ideal, but it works.
Hmm. That's interesting. How do you do it? Do you title it an entirely separate series? How do you link it with the other "one-off" books? Do you mean that you exclude some of the single books from the main series in order to combine them with another different boxed set series? Like a prequel or something? Is that what you mean? You can't include multiple series on Amazon, to my knowledge.
So I titled the series for boxsets and standalones after the Universe. I have multiple separate series within that Universe as well as a few standalones that don't fit into any one series. So I have Series A with 6 books (series page) and 2 box sets (Universe page), Series B with 5 books (own series page) and 2 box sets (Universe page), Series C with 5 books (own series) and 2 box sets (Universe page), then I have three (soon to be four) standalones that don't fit into Series A, B, or C, but are part of the same world and have shared characters and they are in the Universe Series page.
TLDR:
The box sets and the standalones go into the Universe Series (unnumbered) and Series A, B, and C, have the individual books in their own series pages.