The autopilot system on the 744 is a refinement of the system originally developed for the 75 and 76 family. They were developed as "triple redundant" for their anticipated roles and aircraft capability during the infancy of ETOPS operations. Only two autopilots are required for CATIIb operations. Both of the autoplilots work autonomously and with complete control over their components (read seperation of all systems ie autothrottles if embedded in the autopilot system, pitch, roll, yaw channels, pitch trim systems and the like) until the crew "couples" the autopilots. This is usually done by selecting the non flying autopilot to "command" also, and pressing the button which is usually labelled "land".
At that point quite alot of things begin to happen and both autopilots begin to fly their respective components independently, continously cross checking the other's performance for conflicts until touchdown. There are other things happening as well such as electrical system isolation etc.
The auto throttles on most aircraft are completely seperate from the autopilot systems so it is possible to fly with say the Nbr 1 A/P in command and the Nbr 2 Autothrottle system controlling the throttles. For a better idea of how others are setup take a look at the panels on say and L1011 (the first certified CAT IIIb transport category aircraft), the DC10-30, MD-11, or any of the earlier Airbus widebodies. Hope this helps and clears any confusion.