[Jferrante]

the program banks, if i understand them correctly are so that you can essentially put multiple programs onto the robot at one time. What most teams seem to be doing is having there driver code in one bank, and the autonomous code in the other bank. The first command in both banks is usually to check the auton_mode variable to determine when it has changed. The benifit of this is to be able to write 2 totally seperate codes, each one with its own set of variables and programing space. The downside is that unless the programs have all the same variables in the same order they wont agree in memory and when you switch the codes, until you update the variables, there information will be useless.
alternatively you can do a subroutine for your autonomous or simply put it inside of an if statement that checks the auton_mode variable.