Since you are using it with WRF Portal, all you need to do is set the path to the external workflow manager from within Portal Wizard. Here is a short video tutorial on how to do that:http://wrfportal.org/tutorial-flash/tut ... izard.html
When you run a workflow, you'll have the option (from the drop down combo box) of selecting the "Internal" or "External" workflow manager.
Regarding documentation, the author of the external workflow manager hasn't created it yet. I did, however, just add a little more information to the bottom of this page:http://wrfportal.org/WRFPortal.html
Earth System Research Lab / NOAA