I have said for years now I wish they would just roll all the different orginizations into one group. Roll them all into the DEO (Department of Extranormal Operations) with each branch covering certain areas with the head of each group making up a a cabinet reporting to someone who then reports directly to the President and UN. Each branch would have different projects working under them.
ARGUS - Superhuman capture and containment - Headed by Mister Bones
SHADE - Supernatural investigation (Creature Commandos, Frankenstein, ect) - headed by Uncle Sam
Cadmus - research and develoment (Project: Atom, DSI, ect) - headed by Jim Harper
Checkmate - Covert operations/black ops (Suicide Squad, Project: Peacemaker, ect) headed by Amanda Waller
The DEO board would be made up the 4 heads reporting to Sarge Steel who oversaw the whole shebang.