I see what you are saying, but I don't fully agree.
Unless you are having a technical character studio problem, the animation will be done the same way no matter what rig/deformation system you use.
Having said that, there is no one right way to animate. The tutorial I linked deals with one way and also explains a lot of the basic concepts to consider when starting a run cycle.
I suggest reading thru it and trying to apply it to your character studio rig.
If you need help using the character studio rig, let us know because that is a different topic and someone might have a good tutorial for that.