[AGPapa]

There are no rules prohibiting this. However, I don't understand how you plan on doing it. Do you want these controls on the front panel of autonomous.vi? How are you going to edit those controls once the code is compiled? Or do you plan on recompiling your code whenever you want to change the autonomous routine?

A simpler way that doesn't require you to recompile code is to use the digital inputs on the driver station. The default autonomous.vi already has code to read from the driver station's digital inputs. Just click on a different button before each match to select which auto mode you want to use,