Sometimes I write my class notes and assignments in mathematica. I'm over the attitude that WYSYWIG is for dilettantes and come to realize realize I really hate staring at LaTeX code and knowing it like the back of my hand hasn't made me like it any better. So Mathematica I've found to be a nice alternative for simple documents that don't need to look perfect.
The only issue I have is that the stylesheets do not seem to be documented very well---programming stylesheets is documented, just not how to use the stylesheets available. I'm not exactly sure how one is supposed to use the stylesheet to structure the documents.
For example, I use the article stylesheet, and notice there are cell types for Theorems, proposition, corrallary etc. But I havn't been able to figure out if, for example, the "Theorem" cells are meant for the title/number of the theorem, or for the actual statement of the theorem. If it isn't for the statement of the theorem, is the style sheet designed to use the theorem cell to title the theorem, and then the expression goes under it in a regular text cell? If the theorem cells are meant for the statement of the theorem, then how does one label and title the theorem? Has anyone written documentation on this? It doesn't seem to be in the Mathematica database.
Does anyone know a resource for using mathematica as a (quick and dirty) publishing tool? It seems to be undocumented but it has some tantalizing features.
At least your question on Theorem and alike is easy to answer. I assume you have Mathematica 8, have you?
In this case, go to Menu/Palette/WritingAssistant/Writing and Formatting/Stylesheet Chooser
The latter button is placed in the lower part of the upper block in the Writing Assistant palette. Upon pressing it you will bring a dialog up that enables you to see 14 miniature stylesheets. The second in the top row is the Journal Article Stylesheet. If you click on it a template will appear, in which all possible styles are already filled in by dummy words. You will explicitly see the answers to your question on the Theorem style and possible others.
Another story is that the JournalArticle style is not quite satisfactory. The first thing is that it has too small values of the fonts of such styles as "Text" and few others. This means that it makes difficulties to read it, especially for one who has no Mathematica at hand. For example the printed version has a too small sizes of letters, and my colleagues claimed that they simply cannot read my documents done within this stylesheet. If you are teaching using these documents, this might be important. I should admit, however, that I did not try any more, since I made my own style spin off from the JournalArticle. So may be now it is already better: I do not know.
In case it is still unsatisfactory you may wish to modify the StyleSheet you use to adjust it better to your needs. This is, however, a separate question. You may go through the archive, since it has been already discussed several times here, and we may discuss it once more, if needed.