If you search the white papers, there are plenty of good papers detailing the hardware portion of CAN.
As for programming, the provided javadoc in netbeans contains all the details about the different methods. Here is the
same thing online.
You can use
this program from TI to manage your Jaguars. It is useful for testing. Make sure you have a serial cable.
The only thing we used CAN for last year was our shooter motor. We controlled it using the voltage mode, because our encoder/PID loop wasn't giving consistent results. (If you take the time to read the CAN subforums, methods for determining PID constants are detailed). I've attached our [commented] file containing all our CAN code from last year.
Good Luck!