The FTC Getting Started PDF that is installed with the FTC software includes documentation on Program Chooser.
When you select a program on your NXT to run in dual-program mode with Program Chooser, that means that the Controller Station/Field Management System will kill whatever program is running on your NXT (if any) and run the program you selected when the match mode changes from Autonomous to Tele-Operated. Program Chooser will not cause anything to be put onto the NXT - it only allows you to select from programs that are already there. Teams are always expected to manually run their own autonomous program and use the Enabled/Disabled flag to control when the robot actually starts moving.
Ramsey Nasir Senior Software Engineer, InsightCM R&D National Instruments