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Best option is using epubsplit. I have been using it for omnibuses and even short stories now if a ss collection has stories falling in different times between books.
As far as spin offs go I usually use hierarchical series that way I can have all the books in one series but divided by sub series. Depending on how the series timelines go I either use the number after . period for the numbering of sub series and the number before the period for the timeline.
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