Given a date object:
date.getFullYear().toString().substr(2,2);
It returns the number as string. If you want it as integer just wrap it inside the parseInt() function:
var twoDigitsYear = parseInt(date.getFullYear().toString().substr(2,2), 10);
Example with the current year in one line:
var twoDigitsCurrentYear = parseInt(new Date().getFullYear().toString().substr(2,2));