Thanks for the help. I'm still unclear what the ADE library is for, since it seems the Sony Library handles DRMed files. It seems redundant, so I haven't even opened it since it first got installed. At least I can use it to avoid the Sony Library, so that's a good thing.
As for #4, what I'd like to do is find out why I have 48 books in my Calibre library, but 57 books on my reader (or vice versa). I think in other database applications, you can do a comparative search, and find things that are in one table but not in the other. Right now, it's not too hard to compare back and forth (i.e. item #1 is here, is it over there? Yes it is. Now item #2, I have it here, is it over there?) At ~50 items it's starting to get a little cumbersome to do that. Once there's 100+, it'll be even harder. So I'd like to search for books that are in one table but not the other.