Will Theme-It work with PHP/HTML/CSS Pieces

I have several websites where there is an index.php that calls for all the pieces to the web pages. In this index.php are variables for css, js, html, etc. The html pages ONLY have text, images, and other objects pertinent to that page. There are no links to external files to the html pages (w/ exception to javascripts related to individual pages).

Can Theme-It still work with pages laid out like this? The only way I can currently make certain that the pages work is to load all the pieces onto the server and view it with the browser.

I currently use Dw CS4, but I'm new to it, so this is all a learning process. I am still unsure how to use the template option with Dw. All my PHP/HTML/CSS sites were hard coded before Dw.

Thanks for your help.
Heidi Hafner