I got your pm your website seems to be working fine for me. You probably did a custom installation since you have it on your main domain and not a sub-domain (which is the only way with simple installs). Have you tried looking for a wordpress plug-in that will make it easier for you to add affiliate links? I think you should use a plug-in instead of manually editing your wordpress files if you don't really know what you're doing.
This looks promising:
Also this one might be useful as well but I don't know if it would work with the latest version (it just says you need version 2 or higher so...):