Should I capitalize the phrase that has its abbreviation following?
Solution 1:
The US Department of Defense began operation of the Global Positioning System back in 1993, following development of the Navigation System with Timing and Ranging (NAVSTAR) in the early 1970's. Today, GPS, as we know it, is owned by the US Government, and managed by the US Air Force. All of these organisations refer to Global Positioning System. Furthermore, the GPS Standard Positioning Service (SPS) Performance Standard document released by the administering authority refers to the capitalized version. So, I don't believe there is an argument about that one.
For other self-coined phrases, it may be a different case. Take for example ATM, ABS and DIY - there is no case for capitalizing the words as they are simply abbreviations of a common phrase. If, however, you are wanting to identify some specialized item (or are a cunning marketer), you might want to capitalize the phrase. I think "Augmented Filter Subsystem (AFS)" has a better ring to it; far more worthy of a patent or higher dollar charge.
Solution 2:
"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.