If you bring up the ProjectExplorer window, scroll to the bottom of the cRIO target, and expand the last item (Build Spec's). Right-click on the FRC Robot Boot-up Deployment. There are many options in there ... First you "Build" it. Then you "Set as Startup".
There's also some interesting information under the "Properties" option, but I don't fiddle with them, I just look at 'em ...
[edit] ... nice one Mark ... I should've hit refresh before I replied!