I want to clarify some terms, since that can vastly change the answer. In the Republic of Vietnam (South Vietnam) we can separate the militants into two categories:

1. People's Liberation Armed Forces (PLAF), which was the armed counterpart to the National Liberation Front. These are the 'Viet Cong'.
2. The Democratic Republic of Vietnam's (North Vietnam) armed forces, the People's Liberation Army or PLA.

PLAF was primarily southerners, though there were advisors and political cadres serving within it. But the average soldier, as you say, was from the south. Conversely, the PLA was a northern based professional army composed of DRV citizens. After 1968, they were playing an increasingly larger role in the war. It was this force that won the war. PLAF alone was not capable of winning the war. This much is not in debate.

Historians do differ on the degree of autonomy that the NLF and PLAF exercised in relation to the DRV and PLA. This debate will continue as long as the DRV documents are restricted by the current communist regime in Vietnam -- in other words until there is a revolution or change of government and the Vietnamese Worker's Party falls from power. What's not debatable however is that the NLF leadership chose to follow the DRV's policy in large measure (most were former partisans of the DRV during the First Indochina War) and that it directly facilitated the control of the DRV, not the NLF and its 'Provisional Revolutionary Government', over all of Vietnam.

A recent book on the NLF, with some limitations due to the author's staunch Orthodox perspective of the war, uses interviews with captured prisoners to describe the NLF. David Hunt, Vietnam's Southern Revolution (U. Mass., 2008).