I think someone will have to make him the corpse/body, inscribed with runes with the skull as a sanctum/CPU. But it's pointless anyway, Butters was stupid to have Bob out in the open and fighting. Too vulnerable, and if a wizard of Cowl's calibre could separate the skull and lay a hand on it, he'd possess all of Bob's knowledge, which even without Evil Bob's portion is considerable.
If it has to be like this however, a failsafe should be inscribed in the runes, to destroy the skull if it were ever separated from the body, preferably violently enough to kill whoever steals it. RiP Bob.