IE Conditional Comments in PHP/CSS?

I’m experimenting with CSS layouts, and I’m having a terrible time getting them to work in IE. I’d like to use conditional comments like so:
(!--[if expression]) HTML ([endif]--) *
to specify certain things for IE, but they seem to work only in HTML documents. Since all my WP files are either CSS or PHP, I’m at a bit of a loss. I’ve seen these conditional comments used in PHP files (WP blogs, even) before- is there something you have to put in the head tag to get them to work?
I know know how much the URL would help, expecially since it’s just a test page I set up to try the stylesheet on, but there it is: http://www.lodenocity.com/layout-three/index.php
*Replace ) and ( with > and <.