Using a name other than your legal name on an article or book in order to protect your identity or the identity of people included, or when the author wishes to remain anonymous. When submitting your manuscript, put the pen name in the byline under the title, and your real name in the upper, left-hand corner along with your address. If they purchase the manuscript, they will make the check out to the name in the left-hand corner, and the name under the title will be listed as the author when the piece is printed. It's always a good idea to include a cover letter with the submission explaining the reason for the pen name. Publishers generally honor your request to use the pen name, although a few refuse on ethical grounds.
There are a number of different reasons for using a pen name: (1) If the subject matter is of a sensitive nature and you want to remain anonymous, or need to protect the identity of family or friends involved. (2) If you sell a lot of manuscripts to one publisher, they may want you to use a pen name on some of them so it doesn't look like too much of their content is written by the same person. (3) If you are writing in more than one genre and you want to avoid confusion among your readers as you switch from one to another. Or, (4) if you are a man writing in a predominately women's field, or a woman writing in a man's market. (5) If you have a strange name or one difficult to spell or pronounce.
Generally, you will want to use your own name as you build your reputation as a writer in relation to your topic, so only use one if there is a good reason to do so. For tips on how to choose an appropriate pen name, go to: http://www.writing-world.com/business/pen.shtml.