I usually look at other programs that are out there that yours competes with. Take a look at their documentation (especially the table of contents), and do roughly the same thing. Don't steal, just get inspired by it.
How you will write the documentation depends upon who will read the documentation. If you're writing documentation for end-users, making it easy to understand and use is best. (Think of LEGO instructions)
If you're writing for developers, you will need to get a lot more technical with listings of each class, function, method etc. and examples of their use.
You can use something like
phpdocumentor to help if you have good docblocks in your code.
Just my 2 cents.