can´t be called PCB design software...
I don't think that could ever apply to Altium
It does have Atmel libraries, but it's almost as easy to roll your own. To install libraries pop out the libraries thingy on the right, click "libraries" then "install". You should find all the libraries under the Altium install folder.
You can make your own as well, I make new components every second day, it's quicker than looking for one. But it's so long since I created my library I can't remember how to do it.
All above for 2009, but I assume it's the same.