Plans have currently shifted a little -- autocomplete is already handled (better) by combining BBT auto-export with the existing BibTeX auto-completers for atom; the zotero-citations plugin instead has implemented the Zotero citation picker directly callable from Atom; the Zotero picker has autocomplete built-in.

You can set up BBT to auto-export BibTeX (https://zotplus.github.io/better-bibtex/pull-export.html), and then use one of the BibTeX auto-completers such as (https://atom.io/packages/autocomplete-bibtex) to use the exported file. The result can be run through pandoc for conversion to a plethora of formats.

If you don't actually want to use BibTeX and you want to do the whole inside Atom, you can use atom-zotero-citations (https://atom.io/packages/zotero-citations) combined with a running BBT to expand the citations and bibliography (Atom command "Zotero: scan") or to interactively select and insert references in the text (Atom command "Zotero: pick"). Doing the latter will pop up a new window (the Zotero citation picker) where you can select and format your references and atom-zotero-citations will insert them in markdown-format in your text.

I don't have documentation for the picker as I didn't write it; it's Zotero's picker, I just pop it up and grab the results. But it's fairly intuitive to use.

Hello,
Are these processes intended to work with Zotero 5?
I try to set up Atom, Zotero and Markdown.
Thanks for your help,
Frédérique

Thank you for your answer, I will set up something with pandoc then.