I've got around 4000 ePub files in My Documents, all put there via Calibre. I have Calibre set up to send the files to my external microSDHC card, with the following path:
Calibre/{author_sort[0]}/{author_sort}/{title}-{id}/{title} - {authors}
There's a limit to the number of 512 files/folders in the root directory of a FAT16 filesystem (I'm not sure, but I think the internal memory is set up as FAT16), so I would recommend that you set it up so that you don't have the path start with a {author_sort} or other Calibre varaible.
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