I don't think I have adequate help for this applet. Here is a capability that the user should know about, though:
On either of the graphs displayed from the "View" menu, clicking and dragging the mouse will draw a box. The next click will drill down so only that region is displayed on the two graphs.
The "Reset" option on the "Run" menu resets parameters to the default menu. If you have drilled down far enough, you might to use the "Set Parameters" option on the "Run" menu to increase both the transient iterations and the iterations after the transient iterations.