Boston Dynamics keeps making great robots, however, I dont see any papers that they publish. Although now I can find papers on people using the ATLAS robot, I can not find an original paper detailing the robot or its mechanics designs. Is there a reference for the robot, should I use youtube videos?
What kind of "reference" do you want? Some bibtex to reference in your paper? Or detailed schematics?
If it is a paper reference, i'd probably just point to either BD's website above or this: http://www.theroboticschallenge.org or this: http://www.theroboticschallenge.org/files/ATLAS-Datasheet_v15_DARPA.PDF.
If you want to look at their mechanics, take a look at the ROS URDF and gazebo models. They can be downloaded from OSRF's bitbucket site: https://bitbucket.org/osrf/drcsim.
Not really a solid answer, but...
Boston Dynamics does publish papers, though the only one I could find was the one for the BigDog: http://www.bostondynamics.com/img/BigDog_IFAC_Apr-8-2008.pdf
As for the ATLAS robot, it is nowhere to be found, but I believe that as soon as they publish it (if they ever do), it will be on their website http://www.bostondynamics.com
I'm sure they publish, and I bet you can't find anything because they're sponsored by the military. When I was in college, any research that was paid for by the military typically came with a rider that our theses and dissertations had to be made private for 1 year, and that was the longest the university would allow them to be withheld. I'm sure if they could have gotten more time they would have demanded it.
That said, Boston Dynamics is a company, and I'm sure they are competing for funding, so I don't know that they are as comfortable demanding a short time line as a public university would be.
My advice would be to file freedom of information act requests to see if you can get any papers, if you're really that interested.