Your cover letter and any correspondence uses your real name. The information at the top of the first page of the formatted manuscript gives your real name, address, etc. Then you have the story's title and "by Pen Name" in the manuscript's body. Your header will number the pages with a one-word version of your title, your pen name, and your real name: Pen Surname (Real Surname), TITLE, page number. Example: Twain (Clemens), SAWYER, 74
Publishers are used to this and it'll be clear to them.
Maryn, who uses a pen name