ShapeShifter:
Pick a company, use their software, and use their web site/forum as your primary resource. Then, when searching other sites, assume they are talking about the arduino.cc version, since it has been around the longest. But be aware that there are different versions out there, and that some details may change. (The big three differences between arduino.cc's and arduino.org's firmware that I'm aware of are the default WiFi name, the default password, and the default IP address.)
The Yuns offered on the online store at arduino.cc are branded arduino.org!