Clean up a web-site and write a couple of php scripts

I have a javascript/php website that I'd like to customize dynamically--- based on certain input parameters e.g. user logged in, different options should be displayed. A version of the website already exists, so this is really about cleaning up and rewriting parts of it. The big changes needed would be looking up a table to dynamically figure out which options are triggered, and so should be displayed to end user.