Not sure if we file notices when work is done on a military base, what is our coarse of action in this situation to protect our interest when we are a Sub-Sub contractor
For both federal and state-level projects, the ultimate payment security for sub-subcontractors will be a potential claim against the project's payment bond. By and large, military projects are considered federal because the military is generally controlled by the federal government. Granted, for a state's National Guard bases, it's possible they're jointly controlled which could very much complicate the claims process. This article helps with discussion on project type and why it matters: Types of Construction Projects & Why They Matter.
If the project is a federal project, and most military base projects should be, then no preliminary notice will be required. Preliminary notices aren't required to preserve the right to make a bond claim pursuant to the Miller Act. More information on federal projects and Miller Act claim requirements here: (1) Federal Miller Act Guide, Forms & FAQs; and (2) Preliminary Notice Requirements on Public Works Projects.
With that being said, it's generally a good idea to send preliminary notices whether or not they're required. More on that here: Why You Should Send Preliminary Notice Even If It’s Not Required.
Note, however, that if the project happens to be a state project and bound by Washington's public works and bond claim requirements - notice will be required. More discussion here: Who needs to send a Washington preliminary notice on public projects? This article may have valuable information as well: Preliminary Notice Requirements on Public Works Projects.