We were able to deploy from Eclipse to the cRIO
last year. The wpilib build tool is based on
ant, so it runs directly inside eclipse, no problems. You will need the cRIO version of wpilib, however.
You'll need to tweak your
.sunspotfrc.properties file to have the path of the old wpilib directory, as well as the remote address of your robot. When building from ant, you'll need to specify the remote address as a system property: e.g.
-Dremoteaddress=10.te.am.2
When deploying, the ant build script will FTP your code onto the remote address.