[Vikesrock]

The typical way to do this is to read the switches (whether on the robot or the Driver Station) at the beginning of Autonomous mode, then use a Case Structure to choose which code to run based on the input.

You can see an example of this behavior in the default Autonomous code. It is setup to use 2 switches attached to the Cypress PSOC on the Driver Station in order to select between straight, left Y or right Y. In the default code the Case Structure only effects a small portion of the code, but it is often wrapped around a larger chunk of code to switch between very different autonomous modes.