I write a lot of my stuff in Byword, Drafts, or 1Writer and then simply copy and paste into Word for sharing with Windows users (or into Pages if it’s not for sharing but I need to print it formatted in a specific way). Most of what I write requires very little formatting, though, so it’s pretty easy.
I’m ok with a fairly straightforward workflow but I’m struggling to produce something with headers, footers, footnotes, table of contents, page numbers etc. Think I’m stuck Word
You’re not stuck with Word. There are a ton of markdown apps with good MS Word export options. iA Writer, as @ldebritto mentioned, Ulysses, Bear, and many others. Plus as @anon41602260 said, on the Mac you can always save in .md format and convert using Marked 2.
I write most of my stuff in iA Writer (and occasionally Ulysses for longer documents) and export to word when I need to work with colleagues who are used to that format.