Is there any way of specifying a priority for either definition or instance of the process to be more important than another.
No, but since jBPM is a very lightweight engine, you can run several in parallel for different processes (you can even embed one in each application) and make sure one runs more e.g. jobschedulers then the other. Or you can take other measures to signal one type of process instance more often then another (e.g. by using jms queues with different numbers of mdb's on them). So I advice to atm use existing JEE options.