In ROBOTC you can generate a template that is a single file with two tasks, one for driver control and one for autonomous.
The Cortex actually has a user processor and a master processor. The master will tell the user processor when to start driver control and when to start autonomous during the competition. This is done over a shared SPI link.
In reality the competition controller signals the master processor over VEXnet, which then propagates that to the user processor which is running a kernel that handles it. In the case of ROBOTC this is handled by stopping and starting the appropriate tasks.
You don’t need to worry about all this.
In ROBOTC just create a new project and fill in the autonomous and driver control tasks.
You can trigger these modes with a competition switch.