In the dependencies part of your bower.json you can have something like this:
"dependencies": {
"jquery": "2.0.0",
"jquery-1.9.1": "http://code.jquery.com/jquery-1.9.1.js"
}
One shouldn't normally have to do this, but sometimes you have to maintain / migrate an existing website that (for whatever reason) uses different versions of jquery in different pages!