Latex is the standard package for formatting papers in mathematics and computer science. It takes a bit more patience at first than Word, but its output is much prettier and it is vastly better at handling mathematics, inserted figures, and bibliographic references. If you end up going to graduate school in computer science, you will eventually have to learn Latex.
The standard Latex manual is the 1994 book by Leslie Lamport. Several other books have appeared since then: do tell us if you have opinions about which are good/bad. Here is a quick guide to writing equations in math mode. And a a second short-guide.
Don't try to create your first document from scratch. Rather, try to modify someone else's working example file. A sample document often comes with Latex distributions. Or use the sample document below.
If you find Latex interesting but would prefer an IDE or WYSIWYG interface, you may want to try Lyx, TeXnicCenter, Kile, or TeXmacs.
Some other recommended latex packages:
Here are the slides from a quick introduction to latex, as well as an example document that you can use to get started.
If your submission requires diagrams, you can draw them with your favorite graphical editor. See the homework submission instructions for the regular course for some suggestions. Figures in most standard graphics formats (e.g. eps, png) can be included in latex documents. Here are some instructions on including figures.
It is also possible to draw diagrams in latex. One simple latex package for drawing trees, state diagrams, etc is gastex. (It appears that there may be more recent version than what's on that page.) We can give you examples from homework source files if you'd like to try using it. Here is a listing of commands. You may find it easier to use the jastex graphical interface to gastex.