Oh, Worldwalker? Allow me...
Roryok,
Here is the best explanation I've seen about why you shouldn't be overly concerned about how calibre sets up files. When it's working correctly, the file structure is invisible to you. I can vouch for that -- I have a Sony, a Kindle, and a Jetbook, and I am able to use calibre to manage the books on all three of them without a hitch. I see you have a Nook, and alas, I don't have one of those, but there are lots of Nook owners who use calibre very happily.
You might want to jump over to the calibre portion of the forums and poke around a little bit. There is SO much helpful information there. I hope you can get everything working the way you like it!