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You want to launch mavros to connect your copter running ArduPilot to the ROS network. Once you have that working, try manually publishing and subscribing to topics and see if the copter responds. Then you need to set up rosbridge_suite to run a rosbridge server. Finally, create a Java application that uses that java_rosbridge library to publish/subscribe to topics.

In the end, if I understand correctly, if you were to publish a topic from your Java application the chain would look like this: Java app->java_rosbridge library->rosbridge->mavros->ArduPilot. Ideally run the java and all the ROS stuff from the ground station and use UDP to wirelessly talk to ArduPilot on the copter.