In Auto Pilot mode, the product will take the best decisions for all encountered situation(when a malware is discovered, when a program asks to connect to the internet, etc).
In User Mode, in some situations, the user will receive some pop-ups for some actions like reboot to clean an infection, reboot to install a product update, etc.
We are working to improve the second one to involve the user in more actions and make it more interactive.
I have received several request about this here http://forum.bitdefender.com/index.php?showtopic=36069
and forwarded them to our developers.