There are two main ways to submit to publications (I'm leaving out "being solicited by the editor"):
1. E-mail or snail-mail your story, with a cover letter, and mark your calendar so you know when to query if you haven't heard back. Then wait one-to-three months, only to receive a brief e-mail (or snail-mail) with most likely a form rejection. Or, if you're lucky, a personalized rejection. Or if you're REALLY lucky, like I was with my first sub to Asimov's, a multi-paragraph personalized rejection with a recommendation to re-submit the story and a full-page letter personalized rejection for that one too.
This method includes e-mail forms that just e-mail the story to the editor without revealing his/her address.
2. Send your story into a submission system, such as ASIM or Lightspeed or Clarkesworld (I think they have one; I haven't submitted to them yet). Track it obsessively as the queue number goes lower and lower until finally you're rejected, likely receiving a form rejection via e-mail. Or you might be accepted; it's certainly possible.
Which do you prefer?
I personally prefer #1 because it's more likely that I'll get some sort of personalized rejection; the editor or slush reader has to actually click REPLY to my e-mail and type (or paste) something. #2 is great because you know EXACTLY where your story is, but it can be more painful because you're more aware of the process. The only time I've had truly excellent experiences with #2 is submitting to ASIM -- stories that get to the third level, if rejected, are sent back with reader commentary that can help mold the story into something better.
What do you think?