That would be the logical thing to do, and it is what I have done as I've been developing my sites design. Now I'm ready to start actually developing a template for zen-cart, and I'm completely baffled by its completely uncommented php code. I'm far from a PHP guru, but I'm competent at it, but for the life of me, I've been unable to figure out how their file loading mechanism works. I make the changes to the code, and it just doesn't seem to find the files.
But regardless, it would actually be slightly prefereable to make the change. This way, I can go back & add some php to my older css files without haveing to edit each file that loads them. Given a choice, that would be the preferred solution.