I would say that both, baskata & afo are correct.

Having designed & corrected many Templates, Zen Cart or otherwise and IMHO, it is always best to create your Template as a stand alone HTML page. This includes your CSS, JavaScript or whatever else you want to use. This also allows one to Validate their code and know that everything is correct. From there you can run it as HTML or code it to be used within any script, be it PHP, Perl, ASP, whatever.