One way is to upload the JScript file to the web resource. This will embed the "JScript file" code inside the web resource.
|JS File in Visual Studio 2010|
|JScript File uploaded as part of a Web Resource|
The other way to create an empty JScript web resource. Later open the JScript web resource and add the code through its text editor.
|Web Resource Text Editor|
|JScript in Web Resource Text Editor|