Another helpful tip, I prefix all my tags with a certain character: genres are prefixed with a ! e.g. !Fantasy, !Sci-Fi; types are prefixed with a # such as #Collection, #Short Fiction; sources are prefixed with a - e.g. -Fictionwise, -MobileRead; status is prefixed with % such as %Read and %Unread.
You could thus allocate another prefix for tags which are actually specify sub-series, and as long as you order and number by the main series field (and the numbers are in the same order) the books should all come out in the right order in both collections when copied to the reader.
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