If you load a book from the Sony PC software, it'll keep a copy in that library, so you don't need to worry about copying them back from the Reader to your PC.
I keep a "My Books" collection on my 500, that I use as a reading shelf. I use a collection instead of just the "Books" menu because the collection allows me to put them in the order I want -- especially nice for series. I also keep a couple of other collections on it that let me separate out some specific titles from the rest for various reasons. I rarely have more than six or eight books on it at a time.
As for long term storage, I tend not to keep books in the Sony Library at all, mostly because there's no real way to organize them within it. Sure, you have the collections there too, but if you want to do anything other than load them onto the Reader, you have to go back to the main books listing, which is in plain old alpha-by-title order, which gets annoying to me
real fast.
What I did was set up a series of sub-directories, one set for Sony texts and a separate one for books from other sources (helps me keep track of which ones are DRM'ed, you see). I sort the books by author name (nothing clever there), and I'll subdir series to group them. I also tend to prepend a series order number, 01, 02, etc. to those to keep them in order. If a series or book is co-written, I'll put links to it in the other author's directory so I can find it however I go about looking.
On the Sony books, I change their file names from the indecipherable ones that they come with to the book titles -- this doesn't affect the way they work on the Reader or the Library software at all.
If you're not doing a lot of Sony books, you can also try Calibre, it has an organizer built into it, I believe. I've not tried to use it to organize my own books because I already had my system worked out when it came on the scene.
