Do they launch/recover autonomously and fly waypoints or is there a pilot in the loop?
The autopilot is always flying the airplane. For the Blackjack a pilot can command altitudes, airspeeds, RPM/Throttle settings, and can use something called Control Wheel Steering to get the airplane to maneuver left and right to certain angles of bank, in addition to create routes, waypoints and orbits. However, the autopilot is always flying the airplane and it won't let you exceed certain parameters.
The launch process is pretty automated- you command ready to launch and when the PC hits the button on the launcher the thing follows the programmed logic to detect the launch and climb away. Recovery is a little less automated, but it is mostly preprogrammed- as in you edit and load recovery parameters for an approach then fly it. You have the ability to command a few things (for wave-offs) but the only thing you really hawk is airspeed. You essentially get one control (AS) to help manage glideslope, closure speed and crab angle. It's not a perfect system, but it works- and it's cheaper than training someone to hand fly.
Most of the brainpower is spent on the sensors (which is a good thing), and everything else is a scan. The hard part is having to be ahead of the little robot all the time, because you can't do any rapid maneuvering to get you out of a tight spot. That and learning that for better or worse the robot is going to do exactly what you told it to.