if you want to change the colors of anything in the forum this can be done from the configuration file config.php.
if you want to mess around with the HTML of the posts and pages itself, that would pretty much all happen in body.php and bod_post_view.php.
all the files that have a name that starts with "bod_" are HTML that decide what the forum looks like, pretty much all the logic is in the "pre_" files and the other files.
so in other words, if you want to change the way the forum looks, you can safely mess around with the "bod_" files. and to change the look of the navigation bars at the top, you need to edit body.php itself.