I have had about forty articles published, the majority in modeling mags. In the trade, there is what is known as a query letter. This is a proposal as people have described above. Smaller mags are quite informal and will consider a submission without a query, but the bigger, older mags like the detailed query. I find FSM is okay with email proposals.
In big general circulation mags, the editor would then give you an assignment, which is kind of contractual. If you submit an article and it no longer meets their needs, they still send you some money. I don't know of any model mag that does that. Basically, they consider what you are submitting is what is known in the trade as speculation, where you do submit an article without a firm query response, and they may still buy it. I always include in my query that I write on spec, and the editor is not obligated to do anything except look it over, and pay me if he uses it.
As far as submitting a manuscript, I still mail in the subscription. I submit the text, a thumbnail of all the photos, a hard copy seperate list of photo captions, and hard copy of any miscellaneous items like sidebars. I also include a data CD or DVD with an article text file in .doc format, other files I have mentioned (captions, sidebars, etc) on the disk (photos in jpeg, other text in .doc).
The trade used to require a stamped SASE for the return of the manuscript. Nowadays, with the ease of reprinting the material, I merely say in the cover letter to the submission, that I have not enclosed a SASE, and tell them to destroy the manuscript if they do not use it.
Editors used to prefer the text submission in a particular font and doublespaced. I don't know if most mags still want it this way or not. I just use times roman, but I do still double space. Most mags do have a handout on their preferences. It used to accompany the answer to the query. Now adays it is frequently online. If you cannot find it ask in your query letter if they have a submissions guideline.
One last item. Do not staple the pages of the submission. And make sure each page is numbered, has your name and info on it, and the title of the article or what is known as a slugtitle- an abbreviated title.