I'm a little late to this, but I just found a great introduction if you are looking for a guide to using Java APM from the folks at SCOMfaq.ch.
- Part 1) Creation & Discovery of Ubuntu Linux VM
- Part 2) Discovery of Java Application Servers
- Part 3) Java APM
December 17th, 2013: Updated Links
If you are looking for a good overview to help you through an installation, this is going to be a great place to start!