I would recommend using a card reader, just waiting for the illiad to turn on and establish a connection is a pain.
Breaking them down into directories is how I list all my Texts, you can assign custom comments and images see here for a how to
https://www.mobileread.com/forums/sho...d+manifest.xml
and if they happen to belong in two directories, maybe just include them in both, if you buy an 8gb flash card your not going to run out of space any time soon.