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Calibre does not organize by series folders. As a matter, you do not need to even know what the Library folder structure looks like (and never touch it or you break linkages).
Tags: are how you classify. Cookbooks, steampunk, Religion...
Series: (and Series_index) are how you track their order. Note:There is only one that can be set per book. Some folk make a custom column (series like) for a second. I chose the Hierarchical to breakdown a single universe. Pern,Harper Hall
YMMV
Authors has a column. & between if multiple Jon Smith & Mary Smith
Custom columns can be used for just about anything there is a regular one of.
I have a #usertags column, that I add a Tag for the store or source.
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