I am fairly new to footwear study so I am struggling to figure out how to make a multi-segmental footmodel work in shod conditions. I am looking at using the IOR model (as per Visual3D) but, I am really struggling to get good visibility of the markers during motion capture. Especially the base and head of the 2nd metatarsals and the sustentaculum markers. What makes things even more interesting is I am looking at agility movements, so that makes the shoe interfere with the markers (when it is visible). Cutting bigger holes will probably diminish the integrity of the shoe.

What is the best practical way to go about this?