I would suggest you get a hold of a researcher who has a lot of experience with FOIA requests. There are a few that have mentioned they would help others with filling out FOIA requests correctly and give them the tricks and tips to get the best response.
Another consideration to consider is using the correct terminology associated to the subject you are inquiring about. The military and government branches have very specific terms for everything, usually followed by nick names. So, for instance, if you wanted information and documents on what is commonly called "UFO's" you would get back only documents with that term, while if you use the term the military uses for what we call UFO's, which is "UTC's", you would get back much more material that better represents the intention of your inquiry. So I suggest you research the correct terminology for underground bases that each of the branches use. Also, find out which branch(es) would be tasked with the project. Thenyou might be able to stumble upon the project name of some of the underground base builds and put in a FOIA for those projects.
I very much agree with Shamangineer in that government projects are largely outsourced to private companies. The way the laws are written private companies are allowed a substantial amount of privacy to protect trade secrets, processes, technology, etc from being copied, or even hinting at anything that might lead to a loss of profits or additional costs. This allows the government to outsource government projects to private companies with contractual agreements to accomplish their goals. This makes it extremely difficult to gain access to any information at all. But there is still information you can access that might be useful or what you might need to prove your point.
Good luck.