If this helps, there is a dipswitch on the cRIO that is readily available for user use (a light too). If you only have two types of autonomous modes, you can use that switch to change modes before each match starts. In LabVIEW, the VIs for getting the switch state and controlling the light are in the driverstation palette, I think. Someplace like that, look around.
Here's a very helpful manual about the cRIO that mentions these things:
http://decibel.ni.com/content/docs/DOC-2632