Supposed you had the following setup in your WAP project.
In your root you had:
SomeFile.js
Images [folder]
and you had some javascript referencing an image:
iContainer.src = "images/" + s;
You then moved the .js file to Content\JS folder:
Content[folder]
js[folder]
SomeFile.js
and you moved images folder to Content\Images
Content[folder]
images[folder]
The content folder is also in the root of the web project.
Then would you change that javascript to this:
sContainer.src = "/content/images/" + s;
or this:
sContainer.src = "../../content/images/" + s;
I think /content and content/ is the same.