Lately I store research materials for current projects in DevonThink and write in Ulysses. When done I export an archive copy of the article to Markdown and drop it in DevonThink, along with a link to the original sheet in Ulysses.
Very similar to what I do I think. research materials I keep in DevonThink, I could have been clearer about that. I only keep what I am actually writing on the Desktop. I use Ulysses mostly until it is ready for final editing and formatting I might say in LaTeX, which, as I said, I do on Desktop. I put the final pdf always into Devonthink and that is the ‘real’ copy I guess?
I assume the apps themselves are guiding our behavior to some extent. Thanks @MitchWagner for the reply.