Closing PMS with the "Quit" button (that's not a task kill, it's a proper closing) should close javaw.exe. If it's not, please replicate the issue and provide the debug.log
However, if you're running the service (which you hinted you might install), quiting the GUI will not stop the service. To stop the service, you need to go through the standard Services dialog and stop the service there.
You're allowed to run multiple instances of PMS as there are several people who run different instances on different NICs for different devices using custom profiles