If you are using CAN with Jaguars, then you can easily set speeds using their built-in control feedback loop system and plugging your encoder into your Jaguar. For Java, see the
CANJaguar javadocs, and note the "control mode" variable, which you can set to kSpeed, setPID(), and set() method. You will have to tell it how many encoder codes your encoder will report per revolution as well.
If you want to see an example of making your own feedback loops for Victors, you can check out a (Java) class we wrote last year to do this
here.