Most pubs that I've come across seem to prefer its submissions follow William Shunn's formatting guidelines. You'll want to familiarize yourself with them (deferring to individual publications' guidelines for specific preferences.) Save yourself some time by creating a Word doc. with the formatting already in place, so when you're ready to write a new story, you can just save it with the working title and get to work, and not have to worry about the setup. (Word of advice: in my experience, maybe a third of magazines prefer a Word doc., while a third prefer rich text format, rtf., and the rest accept either--as long as it's one of those. So when you're done writing, and you're ready to submit the story, save it in both formats, so you don't have to do it later.)
So, you've gotten your manuscript written to general industry guidelines, and you're ready to kick your baby out of the nest and see if it'll fly. The best way to give it its best shot at being published, is, of course, to find a publication specifically looking for the type of story you've written. Most people will tell you to pick up a copy of the magazine and read it, to see what types of stories it has already published, and submit accordingly. But that can get costly. So I recommend looking closely at the guidelines on the pub's website. It will tell you exactly what the editors are looking for, in addition to their preferred formatting guidelines. Something else it'll tell you? What the editors are NOT looking for. You can avoid a lot of embarrassment and wasted time by reading the guidelines. If you've written a story about glittery vampires, that's all well and good. But not if you're submitting it to a magazine that's looking for something along the lines of 30 Days of Night, or The Strain.
Another thing the website submissions guidelines will tell you: if they're open for submission. Or unsolicited submission. Or when they will be open for submission, and for how long. Maybe they take simultaneous submissions (meaning it's OK if you've submitted it to another publication at the same time), but not multiple submissions (sending more than one submission to the same pub). Or vice versa. Or neither. (Just this morning, I submitted to one magazine that was fine with both.)
Do you see what I'm saying? In an industry where everyone and his or her proverbial grandmother is blowing up in-boxes with manuscripts, you have to be smart about where (and when) you try to place your little gems. Which brings up one last thing.
If it seems like submitting stories to magazines is hopelessly complicated, there are reasons. One, submitting according to guidelines makes it easier to read, edit, and ultimately print your story without having to, in effect, reinvent the wheel. So, all things being equal, if it's a choice between a submission that has all the formatting in place, and an equally good story that will have to be completely reformatted, then guess which story will be chosen? Right. Exactly. Which is why some people (myself included) think of these guidelines almost as an IQ test. Submitting according to the publisher's guidelines marks the writer as a serious professional who can follow directions. Submitting manuscripts that, even at first glance, is completely off the stated guidelines is quite often enough in itself to cause an editor to move that story from the slush pile to the circular file.
I may talk later about organizing and tracking the submissions process. But for now, I've got a couple of flash fiction pieces that need to go out and make me some money, and daylight's awastin'.