I’ve tried increasing substeps, but still my object is penetrating the collision object. I would make the markers more accurate but my character is a single mesh so I can’t map individual meshes to the markers. Are there any other ways I can stop this from happening?
i think the best way would be to model the parts of the mesh - simple cages are enough and your collisions will look good
Hm, very hard to know without seeing what you are seeing.
But for splitting up the character into individual pieces, have a look at this tutorial.