[Chris8]

vBulletin forum isn't a simple website, it has very complex functionality, combining all javascripts into one and css stylesheets into one might not be best thing to do. Also it may cause completely opposite effect because one stylesheet may load on one page while on another may not be necessary, same for javascripts, so when all of it will get loaded on every page the result may be reverse - it may take much longer to load a page. Better thing would be to minify everything what is not minified.
But to answer your questions, as for CSS it always go to head of the site so -> headinclude, javascripts not necessarily, but usually they go also into head bellow styles.