Sony Reader Library was rather slow and sucky with the older readers, but they have greatly improved it to work much faster with the new readers (350 and 650). It is the easiest way to get books onto your 650 and into collections.

You can also use calibre, but there is a learning curve.

You can also add books directly to an SD card, but they won't show up in collections. However you can assign the books to collections using the 650 menus.

You can also copy books directly to the 650 from your computer with a USB connection, but they won't show up in collections. However you can assign the books to collections using the 650 menus. To copy directly find the drive for your reader, mine is drive N:, then copy books to the following path:

READER N:/database/media/books/