I\'m running into the typical virtual-directory dilemma in that you have some paths on your ASP.Net application and you deploy the app in a IIS virtual
Are you using the tilde (~) for your paths where you can?
~ refers to the root of the virtual Web application....
~/images for example.
If it's just for css files on the client side then using the url directive makes the path relative to that of the style sheet rather than the page:
h1#title { background: url('dog.gif') no-repeat 0 0; }
Also if you're on asp.net mvc then you have access to:
<script src="<%= Url.Content("~/scripts/new.js") %>" type="text/javascript"></script>