As for how to set up LaTeXiT to work with text editing Mac-wide, including Scrivener, this post has some tips. Do note that this post was written for someone who was composing a .tex file in Scrivener, and so everything below the Better Compile Output heading should be ignored. That specifically describes a technique of using LaTeXiT to give an author a visual copy of an equation in the editor that doesn’t end up in the output.
As @kewms notes above, LaTeXiT—as a simple utility for embedding typeset equations into documents in a way that the equation can be edited later—is something that works with almost every text editor on the Mac. Anything that can store an image in the text can work with it, and it is very simple to use. With a little setup, putting some keyboard shortcuts on Services, it can also be very efficient; almost as much so as MathType was.
It makes a picture of an equation—exactly what MathType did, only unlike MathType the typesetting is very good—and a picture of an equation can be used in almost any workflow, from ePub to PDF to Markdown to ODT. That is why there are no instructions for using LaTeXiT with the template for people writing using LaTeX. LaTeXiT, it is safe to say, has a goal of bringing the quality of LaTeX equations to people not writing in that system. 
@asteckley : Scrivener developers – I know it’s not your highest priority, but hope you can get to actually solving this deficiency in what is otherwise a GREAT tool.
So to be clear, we don’t really consider there to be a solvable deficiency here. Adding an embedded image is one hotkey away. Editing it is another hotkey away. There would only be marginal gains in making that any more seamless, but really that’s not the point. The point is that we would not want to stop making writing software for the years it would take to reinvent this stuff—again solely for the purpose of a marginal improvement in workflow. That just doesn’t make any sense, and we’re never going to reach the output quality of LaTeX anyway.