Funding for Military & Gov. Facilities

I have a question about where the funding comes from for some of the elaborate secret military facilities that are used in the United States.
If they are secret how does one go about asking for funds without explaining what they are going to be used for and how does it get approved. Do they just skim off the top of the categories listed in the graph that is at this site?

www.federalbudget.com...

Here is a quote that is on this site that I find interesting. It may be used out of context to support my idea but I think you will get the idea too that we as taxpayers, since we are essentially paying for these facilities, should have some (even limited) ideas about what is going on there.

According to Mr. Kneeland, "...all dollars come from the people. Where do [you] think Coca-Cola gets the money to pay its taxes, Exxon gets its money to pay the Exxon Valdez fines, Denny's gets the money to pay its Justice Department fines, or even Microsoft gets the money to defend itself? It all ultimately can come from only one place, and that's from individuals."

I realize that this may cause a security risk, but how much of a security risk would it really cause since we as US citizens cannot even come close to area 51?

For something so secret it wouldn`t get listed in the National Debt figures.The whole point about being Top Secret is the fact items are not disclosed.Its gets hidden in infomation that requires security clearance at top level.Sorry to sound obvious but the question ia a bit pointless.

Not only what the previous poster said, but many CIA black ops used to be (and still are) funded by CIA profits from cover businesses that the CIA runs as part of an old or new op. Often, if that business is profitable, they keep operating it, and they have some money from it that does not need to be accounted for.

For example, if an agent was to pose as some sort of importer in another country as part of an op, if the imports were run at at profit, there is new money there for other ops.