I am trying to create several markers along a route from google maps directions. I have already looked into waypoints as an option but based on my understanding of the docum
No. Waypoints determine the path of the route, as you found. You want to put "waypoints" along the route whichever path is determined.
It is possible, and Larry has an example at http://www.geocodezip.com/v3_polyline_example_kmmarkers.html