I have been delving in to the MoGraph module of Cinema 4D for quite a while now, and I'm still only really scratching the surface of its true potential. Combining knowledge I have already, I managed to create a system in which I could construct a tree aslong as I provided the simple pieces of mesh and their axis were aligned correctly for placement on either the polygon surface or vertex normals.
This is only a small example, but now I understand the process to get to this state I can now make larger works involving the same technique. In this particular sample, I was able to restrict the placement of the branches to specific selection of polygons on the main trunk using Make Selection and using that as the Object as apposed to the entire mesh object in the properties window.