[ADMcDonald]

This is a quirk for me, too. Two parts: A) I manage the metadata for the series just fine, thanks. Yes you need to be diligent when you import books, because publishers have no standard for series information. It can be there or not, in the title or in the series or both places. That means I have to edit the metadata for each book that comes in. It's worth it.
B) I have set up plugins and plugboards to manage the directory and filenames of the books when they hit the device as well as the metadata of the book that get reader can see. It used to work. Not sure when it crapped out, may have been before 1.0.

I have a Galaxy S4 SGH-I337 with Android 4.2.2 and MoonReader. I put the books on the SDCard. They get to the Card/books/ directory Ok, but fail to get into an author directory.
Here is what I put in the Android device plugin for save template:
{author_sort}/{series:|[|}{series_index:0>4.1f| |] - }{title} - {authors}
and here is what I get:
Card/books/Rivers of London - Ben Aaronovitch.epub
I do something similar to the metadata with a plugboard and get similar results. The bitch is, it used to work!
I have another book:
Card/books/Anthony, Piers/[Cluster 01] - Cluster - Piers Anthony.epub
and the metadata shows the title as:
[Cluster 01] - Cluster

Any suggestions? I'd hate to have to incorporate all my series' into the title field.