I guess Smed can just act as some kind of supplier for all stems of research, providing subjects and stuff. I'm thinking that he'd ally himself with the minion research division, only because he can provide engineers who can help supplement the horribly mutated creatures with crude, mechanical add-ons.
As for rank, I'm not quite sure what this would be called, but something along the lines of a primary resource supplier, or something like that. It won't require him to actually command anything inside the Order, but he'd still attend all the meetings and stuff.
I had the Anklehacker confederacy envisioned as more or less allies of the Order, not really full members, you catch my drift?