You may need to use the Story for a few days before you get a hang of it. Takes a bit of experimentation.
About the long titles that flow off the screen, well I've got the same issue with another reader that I have. I've come to accept things that couldn't be changed...
About where to file stuff, you could put them in any folder you create. To access the folders, select My Folder on the left panel. But if you put ebooks in other folders than BOOK, they wouldn't appear in your regular book list.
If you close a book and reopen it, it does jump straight to the page where you last left off. You don't need to make a bookmark.
Have fun exploring it.