The easiest by far way to run a Java app as a service on Windows is by using one of the wrapper applications available. The following snippet is using Tanuki Software Java Wrapper here, which does have a free community edition, and pretty reasonable pricing if you need more (eg: 64bit). There's other options available, such as Yet Another Java Service Wrapper http://yajsw.sourceforge.net/
Setting up the config:
First off, follow the instructions from Tanuki:
From here, the only slightly cryptic part being getting the "main class" set in the application parameters.
Set the following in your myAppWrapper.conf file (add paths if needed):
followed by any other parameters required.
You may need to tweak other settings, but they should be fairly obvious.
From here, test and install as per the instructions.