Debugging
You can run the Java program on the Beaglebone black, and then connect to it remotely for debugging. This lets you set breakpoints, do basic hot code swaps, etc. More info:
Remote Development
To develop on the Beaglebone directly, you have a few options. I think this best option is to setup a file share on the beaglebone black, and use a build script or similar on the development workstation to automatically copy the recompiled class files (or jar file) over to the beaglebone black.
Another option is to set up a file share from the beaglebone to the dev workstation, and run the java program on the beaglebone using the remote class/jar files.
Yet another option is to just do all the development, including compilation, on the beaglebone black directly. However, this is slow and generally not worthwhile for java development.