I have been using calibre with the metadata plugboard, you can set it to rename the title to include series for example. Without that, it becomes difficult to search for a book. Hopefully the devs have already added a couple of missing feature and with the request for collections support it might not be impossible for them to implement them into the future.
Also about the scanning, it will only process the memory when it see's a file change. I haven't tested with a memory card yet, and don't know the behavior with multiple memory cards.