For anyone who has written such a thing, what would you say are some general rules of thumb for writing organizations set up and funded by the government of a major world power (like the U.S.) that's kept a secret from the general populace?
I would think that anything goes however the main thing would be the consequences of letting others no about such an organization. "We will kill you and your family…" kinda thing. What kind of people are you hiring? Upstanding, convicts, assassins/mercenaries? That would change the type of rules the organization would have. A lot of corporations have clauses that require silence and if something is said normally the company quiets it.
Usually an organization like that run by a world power would be a HUGE liability for that country. Imagine how the rest of the world would react if they found out about it? How would this country's own citizens react? Terribly. Probably throw-out-the-old-rulers terribly. So it has to be super secret. This might be a horrible idea, but here goes:
I would suggest making only ONE guy be the connection between the secret organization and the government. So whenever the ruler is like "man I wish THIS thing would get done," the one special guy would give him a knowing look and say "I'll take care of it" without any context. The ruler knows that whatever that guy is doing is probably illegal, but he won't ask any questions so he can't be connected to the dirty work. Then the secret organization is contacted by the one special guy, and this organization has no idea he's connected to a government. They just know he's rich and they fulfil his missions for them.
Or you could have a code word for it, something that doesn't seem suspicious. If something out of the ordinary would happen, they could wipe their memories? The person above probably has the best advice.
Okay is this good?
In my story, there's an underground organization that has members worldwide and consists of hunters who track demons down and protect humans from them. World Leaders are aware of this group and secretly fund their work, this group is only spoke in whispers between members and the demon community. I don't have a name for it yet, it's a long process. The general public don't know that there are demons roaming around and if they encounter one,they usually don't survive. Those that do, their memories are wiped of any event taking place and any evidence of a case on it, it's erased.
One of the problems with a secret organization is that they never actually stay secret for terribly long. What might be interesting is if the organization isn't a secret, but just regarded as a bunch of kooks.