I know it sounds like semantics, but what you described when you said,

" You make a theory (a best guess using what you already know about the natural world) and then devise a way to test that theory"

that is called a hypothesis not a theory. A theory is, to quote the dictionary

"A set of statements or principles devised to explain a group of facts or phenomena, especially one that has been repeatedly tested or is widely accepted and can be used to make predictions about natural phenomena."

There is a diffrence in the way the term "theory" is used by the general public and the scientific community. A theory is not a blind guess in the dark, It is an accumulation of facts and proven hypothesis' that has been rigorously tested by peer review, subsequent publication of your theory in a scientific journal and duplication and even more tests by other scientist.

That's not to say that theories are infalable, if they don't fit right into other known theories, can't be duplicated, or other theories come along that fit better then the old theory eventualy loses credibility and acceptance.