I am preparing to submit my first research paper to a peer-reviewed journal and am at the stage of writing a cover letter to support my submission. I am technically affiliated with 2 different organisations: the non-academic research organisation where I am physically based and employed by, and the university with whom I am doing my PhD (this paper will be a chapter in my thesis).
I have both as affiliations against my name on the paper's title page, but which should I choose to have as my affiliation when writing my contact details? From an editor's point of view, does an academic institute appear more 'impressive' or doesn't it matter (i.e. is this simply a formality of needing some form of current contact details)?