I pulled together a set of templates and a build system for writing scholarly articles in markdown and building docx, pdf and html output. See pandoc-build-system.
This allows you to use markdown and a bibtex database, but avoid using bibtex styles (styles are handled by pandoc-citeproc). The ideas and templates were borrowed from Kieran Healy’s pandoc build system. See his GitHub repositories pandoc-templates and latex-custom-kjh.
You will need on your machine: pandoc and pandoc-citeproc, and LaTeX (for pdf output). Note to my students: You can try this out on pearse (in room 206D) easily because pearse has all the installed software you would need (pandoc, latex etc).
Also, just a reminder that my student starter Emacs configuration works well. Just clone it into a brand new ~/.emacs.d folder. Again, easiest on linux, so try it out on pearse.