The Connect Software takes the source file's properties. You'll have to make your changes to things like title and author in the source application.
You can use folders/collections on the Connect Software (make them by clicking the + button at the lower left). The collections will let you sort files in the order you want, rather than alphabetical, and you can drop the whole collection onto the Reader directly. I figure the Collections feature is going to get more use than the generic "Books" section of the Reader OS, simply because they're all in alphabetical in the latter, and it's all
of them, so it'll get to be a lot to wade through really quickly.