LaTeX.org

If you're like me, you've been stuck in the dusty halls of the university system for years, the cynicism etched on your face, a perpetual snarl tugging at the corner of your mouth.

At Uni, we have a site-wide license for MatLAB, which is fine. MatLAB is a good platform for running simulations, even ...

If you don't like the red boxes in the TOC, you can set an option in the hyperref package.

For example, replace
with
This will give all the PDF links in blue, which I think looks quite nice!

You can use counter commands to reset the numbering at the beginning of every chapter.

Here's some information on counters: TeX blog

Also, check out the wikibooks page on equation numbering...
Wikibooks

Perhaps a good first step is to run makeindex and make sure that the index file has the appropriate entries.

Some helpful links:

U. Fl. site

Generating an index