There is the User1 dip switch on the cRIO and we have thought about using this to switch the alliance that we are on if we don't get it from the competition port. In your code you can see what the state of this switch is and use it for your own use.
Here is the CompactRIO cRIO-FRC Operating Instructions and Specifications document from NI, a very useful document. Learn more about the User1 dip switch here:
http://decibel.ni.com/content/docs/DOC-2632