So short answer for subdomains
All you need to do is add:
ga('create', 'UA-XXXXX-Y', 'auto');
The 'auto' will capture all the subdomains (as long as you have your GA code on the subdomains)
Longer answer You don't need to use the auto linker or anything like that for subdomains. That's why universal analytics is great. It writes the cookie to the top level domain. So it will look at .com and not be able to write for that then go to example.com and write the cookie there.
In Google Analytics you can then separate it by hostname.
For cross domain tracking you need to add some of the more advanced and load the auto linker method.
They talk about this a bunch in the beginning of the GA dec developer update http://www.youtube.com/watch?v=nmfUoSyFBSk