Ok, I got your problem, Ja.
In calibre, you can change preferences: the way calibre save to disk or device.
(Preferences >> Add/Save >> Saving books & Sending to device)
For example, I set use "save template" for Saving books like this:
{tags}/{series}/{title}
Then I put tag as category of books. So books will place in folder of tags and series, with title as their file names.
Hope you get some idea :-)
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