Make sure that after installing the Sony Reader Library software that you authorize your 650. Without authorizing it, it won't be able to read protected (secured) PDFs or ePubs. Check the Help in the Sony Reader Library app for instructions. After installed, connect your 650 and start the Sony Reader Library app. Click on eBook Store and then sign in. You might need to register and open an account if you haven't done so already. After you sign is, click on My Account and authorize the 650. You should be good to go after that.

Optionally you can install Adobe Digital Editions (ADE) and authorize your 650 with it for reading PDFs that are protected (secured). But if you already installed the Sony Reader Library app you don't need to install ADE.

As far transferring files, a 6mb file should transfer in less than a minute unless there is a problem. If you transfer using the Sony Reader Library app then it might be slow if the reader isn't authorized or it might be some other reason. But that is not typical. It should transfer fairly rapidly.