If you're talking about a series-within-a-series (e.g. the High Halleck and Estcarp Cycles within Andre Norton's Witch World series) then it's not too difficult. My suggestion is to set up a custom Subseries column. Then you can track the position of each book in both the main series and the more specific subseries. That's what I do, and it works fairly well.
If the two series are independent (e.g. the book is part of a main series but it's also in some kind of "best of genre" collection) it becomes more difficult. Again, a custom column for a secondary series could work, but only if the book only shows up in one of these collections. If you need more than that, perhaps the Reading List plugin could help.
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