I use my real name for all correspondence. (My genre, it's nearly all pen names, FWIW.) I don't mention my pen name in queries until I get to publication credits, and there I give only one or two of the pen names used.
The cover page of a novel, or upper page of a short story, shows my real name, contact info, word count, rights offered, all the usual stuff. The title is in caps, the word by below it, and below that, my pen name.
The slugline for each page of the manuscript is a header consisting of my pen name's last name, my real last in parenthesis, a one-word abbreviation for my title, and the page number, i.e., Twain (Clemons), FINN, 26.
Maryn, who's not yet had anybody mix up who to make the check out to or which name goes with the story