Chris,
You’ve probably notices that there’s an “MMD to LaTeX” option in the Compile window. There’s a ton of info on this forum about using MMD with LaTeX and a number of ways to do it–you need to figure out what works for you. User nontroppo, for example, likes using pandoc, but I find that this is more steps than necessary.
I use MMD to do all the text formatting, section formatting, and image/figure handling, (I don’t use tables, so I can’t say whether MMD syntax for that is sufficient for academic purposes.) I use replacements with my own shorthand syntax for theorem environments, and for mathematics I use LaTeX syntax, but I prefer to use the unicode-math package so that I can use math symbol literals instead of LaTeX markup. This is discussed some here:
[url]Different kinds of annotations with colours]
The big disadvantage is that once you’ve exported your Scrivener project to LaTeX there’s no automatic way to get any edits in the LaTeX file back to Scrivener. But Scrivener is so much better than any LaTeX editor on the market that it’s worth the hassle.