Once you have a completed story, properly formatted, then you are almost done. Paperclip your return envelope to the story. Otherwise I advise sending the manuscript without a cover letter. But DON'T send your only copy of a story. Always keep a backup copy at home.
Accidents happen with the post.
Editors occasionally spill coffee on manuscripts. Start writing your next story. Whenever a story is rejected, send it out again to another market. Don't let the rejection stop you from working on your next story. I have heard of people who sold their first submission, but for most new writers rejections far outnumber acceptances.