So who operated the Enclave? And also I remember something about Helios One, a guy said that the technology there was more advanced than the Enclaves perhaps that technology orginated in area 51 and sorry for not knowing who the enclave was
A currently unanswerable question, I personally believe that the Enclave may at first have been leaderless and instead a loose consortium of powerful people who all looked out for each other, scratched each others backs and such, made sure the Poseidon Energy got the permit to mine uranium in a national park and in return they develop a weapon for the US military. Stuff like that. Maybe later (or from the start, as I say who knows?) they grew larger and had a united goal for the US which they all strove to bring about, the highest people are apart of the organisation and by having all of the authority, they can manipulate the rest of the organisation; say they wanted someone assassinated and so called upon the head of the FBI, NSA, whatever to plant some evidence and get the target killed in a "shootout" for "resisting arrest" or "treason".
I personally believe that they were lead by some form of council of the most powerful and connected members, no matter whether they were politicians, soldiers, business man or what; Presidents come and go after all and the Enclave is by no means legimemately connected to the proper government (at least pre-war, post-war I believe that the Enclave simply ceased to exist outside of the old name), members of one are merely members of the other and usurp their legal, earned power for the goals of the secret organisation.
I believe that the guy in Helios was merely failing to notice the connection between Poseidon Energy, Helios ONE and the Enclave; Poseidon Energy was partically dominated by the Enclave's will, they even built the Enclave's hiding place the Oil Rig.