Um, I think they just did.
Let's say that in Autonomous 1 you want the robot to turn left, and Autonomous 2 you want it to turn right.
Code:
If (Digital_input_1 = 1) then
[Code to turn left]
EndIf
If (Digital_input_2 = 1) then
[Code to turn right]
EndIf
Now, you need to think more about this, because what happens if there are jumpers on both inputs 1 and 2? (someone forgot and put both on). And a lot of IF statements might become impractical if you have 25 different autonomous modes.
Also, make sure there's always one choice for "do nothing".
Don