Backing up the entire librarys, seems to work best for me, once there are a few thousand books, having then in a separate windows folder structure seems too complicated for me. (anything to reduce it to its simplest form)
If I have the library on a computer with no Calibri, I know I can just browse to;
C:\Users\transmit\Calibre Library\Ted Chiang\The Lifecycle of Software Objects (229)
to find that Chiang book I wanted to read, so not really felt the need to have it organised further than it already is.
But each to their own, what ever makes you feel most comfortable.
Importing I do singularly or by Author, then add meta data individually, I like to make sure it's right. A bulk renaming utility helps to get the files in the right format first, ie Title - Author
Images - actually, I just got a program that will bulk edit the images, so once their correct I intend to resize them all in one go, so they look nice when in the cover flow view...
Getting rid of multiple Authors, that's an interesting idea, it would slim things down a bit too. I think I would miss the cross referencing it offers, Say you just read "Junk DNA" by Rudy Rucker, and was looking for something similar if it was labeled Rudy Rucker & Bruce Sterling, then a quick click on Bruce, would bring you to other reads you may like.
I do draw the line at compilations/anthology/collections etc as that would be silly, in those cases just the editor and then a list of the included stories and Authors in the Comments field is fine, and I believe it shows up in searches too.
Not really sure how you would go about finding all books with multiple Authors, apart from the obvious.. looking down the Authors Column and then editing manually....
Good luck with that anyway
Edit: - Actually as you will have to check which is the main Author / the one you want associated with the book, your going to have to do each individually, so just look at the Author Column, and Edit directly by clicking twice on the Name (not double clicking as it will open, but select then click, will allow inline editing on the columns themselths.