I recommend adding a vendor.d.ts
file that consolidates all your external definitions like :
/// <reference path="./jquery/jquery.d.ts" />
/// <reference path="./other/other.d.ts" />
And then you only reference vendor.d.ts
:
/// <reference path="../../typings/vendor.d.ts" />
import $ = require("jquery");
BTW, if you are using tsd https://github.com/DefinitelyTyped/tsd it creates a tsd.d.ts
file for you that plays the role of vendor.d.ts