Specifically to come back to this query:
Yeah, that’s probably the easiest way of doing it, particularly if you want a handy self-contained compile Format you can just archive and restore into Scrivener over the years. The alternative is to make the .tex files for these yourself and stash them in your texmf folder, so that MMD’s \input{...} calls find them. The rest is all naming convention. I did write a short tutorial on how to create your own MMD setups, like you see represented as Formats in the compile sidebar. There is another posting here that pretty much covers the same ground, but does go into a little more detail about separators, what you might find interesting for novel writing, if you want a fancy scene break, or even just a vspace.
Pandoc is undeniably more flexible, but I wouldn’t underestimate how much you can do with MMD’s pretty basic system as described. The user manual PDF is after all an example of how far that can go, as well as how far the Memoir-Book class can go (although I will admit I did come close to stressing its limits here and there—it only barely tolerates the package I use for chapter-ToCs).