FusionReactor has a dedicated feature to track down CPU usage per thread called the CPU Profiler.
This will track CPU usage per thread over time and give you an idea of where your application is resource-heavy.
You can take snapshots for point in time comparison and compare a thread's usage over both short and long periods.
To view more about the CPU Sampler see the documentation.
Not that you will often see FusionReactor thread use a reasonably high amount of CPU time as it is constantly monitoring your application in the background. This is especially true on a low traffic server, as it is doing more work compared to the application.