Lyn, I tried my best (which was none too good I'm afraid

) to answer your question in the entourageedge.com forum. Good idea to post it there!
I copied your whole post and reposted it in the General Forum over there, hoping to get a better answer from those who really know their stuff!
I transfer one to three books at a time, those that I foresee reading soonish, and add them to the PE library, assigning tags at that time, whenever I feel like it. Often I will start reading a book without putting it in the library first, then when I want to use the many functions only available through the library I will add it. This doesn't help you much, I know.
The tags and covers in the library are nice, indeed. And I really like the table of contents on the tablet side. But as far as I know there is no way to put a batch of books into the library all at once, or to keep the tags assigned in Calibre before you copied them over. Would be nice, though, eh??