I agree that things are confusing.

I do know is that if you want to synchronise / backup from a folder on your PC, you can only set this up using the Web Browser (blue icon) and the Browser needs to be running for such synchronisation to occur. If you want to synchronise / backup from a folder on a Pogoplug device, you can set this up from the Web Browser or the web interface, and you don't need the Browser to be running for such synchronisation to occur.