My thoughts :
I stay away from javascript due to it depending on the browser.
You need the html to go with the php - the php dose things server side like querys etc. ( cant think of the word for it ) and the html displays it.
I have a template which has html in it for the header etc. then usees the php to include certain html or php pages depending on the navigtion link.
Not a advertisment but I am trying to explain it on a site I am building
www.rubblewebs.co.uk where I am putting some examples for work I am trying to get.
Anthony