I have done the following in WebMatrix.
I imported jQuery inside my HTML page with documentation of jQuery and successfully enabled jQuery intellisense inside the HT
Usually, in Visual Studio you can use reference directive in the beginning of the file. It will include a script file in the scripting context of the current script file. And IntelliSense will be enabled. Since WebMatrix is microsoft as well, I believe this should work too:
/// <reference path="JS/jquery-2.1.0.js" />
/// <reference path="JS/jquery-2.1.0-vsdoc.js" />
if path attribute won't work, try file attribute.
http://yadi.sk/d/Szhp8tOJNLXYu