Recently, my Clarionmate, Ferrett, wrote a very useful post on how to submit short stories. My submission process isn't identical to his, but I highly recommend that you take a look at his advice, especially if you are a beginning writer, and new to the process of submitting to markets. There's a lot of good information and advice in there.
I would add one thing, and it's something I'm trying to work on in my own career: Let the editor reject your story. Don't do her work for her.
Here's what I mean.
Submission is the hardest part of writing for me. Hitting "send" when it comes time to actually turn the story in makes me shaky, and physically ill. I've never submitted to a market with print-only submission guidelines because I know I would never be able to bring myself to take the envelope to the post.
I don't know why this is so difficult for me. I do everything I can to increase my chances of my story being accepted. I read the submission guidelines, and follow them. I make the story the best I can at that moment in time.
And I understand that most stories, even a lot of good stories, get rejected. No market can, or should, publish everything. Editors are people too, and like people, their taste in fiction varies. I'm not afraid of rejection. I don't enjoy it, but I'm not afraid of it. If I were, I couldn't write.
I'm just really good at talking myself out of things. I excel at finding reasons why the story I knew would be a perfect match for Market X when I was writing it is explicitly prohibited from existing by their guidelines. It's crazy, I know.
So one of my goals for this year is to submit the stories I finish. To hit send, once I've done my due diligence on the market, and let the editor decide that my story isn't a good fit. A rejection letter is the worst thing that can happen.