No, there isn't a specific manual like you are talking about - when you using the vBulletin header/footer, you are using just that - their header and footer templates.
We don't use forum specific headers/footer as we aren't part of the forum and don't have an option to override the default header/footer templates (although this might be a good option).
Because we grab all of our
vB stuff up-front, category by category changes to the header/footer files may not be easily accomplished; but you'd be looking at the header-inc.php file for any changes that needed to be made.