Netbeans' profiler was able to hook into my JBoss server, that was running through Eclipse. I thought the profiler wizard setup was helpful. It asks a few questions and produces a line to paste into the to-be-profiled-application's configuration.
That's all there really is to it. There are a few options about filtering methods and what types of profiling, e.g., memory, threads, CPU timing, etc.
The results we found were about what we expected. It was a good exercise to refamiliarize myself with a profiler though.