"Global Positioning System" is the proper name given by the U.S. Department of Defense to its satellite navigation system. It should always be capitalized, not because it's well-known per se but because it's a proper name. To avoid confusion, you should never refer to a different satellite navigation system—or to such systems in general—as global positioning systems.
As for self-coined phrases, it's basically your call. Acronyms and initialisms are almost always capitalized, but there's no requirement that the phrase expanded from an acronym must be capitalized: "GDP" expands to "gross domestic product" in a sentence, for example. But if it's self-coined, it's yours and you can do what you want with it.
If you want my advice, though, one thing I've learned from 15 years of technical writing is that programmers and engineers like to capitalize way too many things. As a general rule of thumb, if you're dealing with words that are not normally capitalized (such as "augmented," "filter," and "subsystem"), leave them uncapitalized unless they already form a proper name or will be used in (*shudder*) marketing materials.