Czars and Bureaucracies

This article at Government Executive argues that Obama's "czars" reflect and counter a bureaucracy's resistance to cooperating with other bureaucracies. Makes sense, but what happens when the bureaucracies in conflict are the Navy, Marines, Army, Air Force in DOD or NRCS, FSA, RD, APHIS, etc. in USDA? (Though it seems Secretary Gates is reasonably effective in managing DOD.)