Cover & format
I agree with Rich. If you have something worth saying in a cover letter, fine, say it. If not, forget the cover letter. Editors buy stories and articles, not cover letters. I've sold stories to top magazines with cover letters, and I've sold stories to top magazines without cover letters.
My only use for a cover letter now is to list two or three of my biggest sales just to make sure a first reader passes the story or article along to the main editor.
Before that I usually just submitted the story or article, and no editor ever complained.
As for format, it's easier to show than to tell. Go here:
http://www.shunn.net/format/story.html