In order to get intellisense to work with js files referenced on your web pag you need to add a _reference.js file. It really doesn't matter where you put the file, but generally it should be placed along with the rest of your js files. Perhaps in a SCRIPTS folder.
Here is a good article explaining it in further detail.
For More Info: (http://gurustop.net/blog/2012/03/03/javascript-js-intellisense-auto_complete-in-visual-studio-11-beta-the-web-_references-js-file)