Javascript - How To Path When Deploying

We have moved a lot of images and javascript file that was inside class to external Javascript file. In development (Debug inside Visual Studio), everything look nice, all images show, all javascript works and all CSS display perfectly. When we do a package and install with IIS ina virtual directory everything that is pointed by the JavaScript doesn't work.

Question : Since we cannot use the tilde (~) in javascript or in CSS what is the way to display those resources?

Edit 1

The problem is the website is installed with a Virtual Directory and if we have in the JavaScript file a popup that has a hardcoded path in the JavaScript the code try to display : "http://localhost/NameSpace/Directory/File.html" instead of "http://localhost/VIRTUALDIRECTORY/NameSpace/Directory/File.html". Is there a configuration with IIS or inside the code I need to add something like a parameter to pass the path everytime?

In the javascript in dev it work to have something like :

var popWindowPath = '/ProgressFile/Simple/ProgressSlow.htm';