No problem for organizing folders on the SD card. You're free.
I have a calibre folder at root level, close to the Sony reader one. But inside, I do whatever I wish, grouping pdf and epub by types and so on
For the pdf, I take care of checking the meta-data with a freeware before uploading. I do not use calibre for it.
Once I had a problem. I destroyed the file called cache.xml and let the reader recreate it again (some minutes because I have lots of books).
To backup files, I use a Linux synchronizing tool called grsync which is very handy. I do not keep either a calibre library.
These are just personal tips I'm happy with. I don't pretend it's the perfect solution.