This has been gone over many, many times already on this board. Please make sure you search the board.
PHP generates HTML, Google WILL NOT see any of yoru PHP code, it will see the resulting HTML, ie the same thing the user sees.
The only thing search engines tend to err away from is long GET variable strings BECAUSE often times they include sessionIDs, and search engines have no way of knowing if they are just sessionIDs and they're indexing the same page only with diff. sessionIDs 30 bazillion times.
If you want to get rid of your query strings, you should look at mod_rewrite, a 404 error method, or ForceType together with a URL parser you write in PHP. Search teh baord for more details and more code.