I’m in the same spot that you are. Let me explain what happened.
I can sign into Skype using my Skype name (of course) or my Microsoft account name/Hotmail address. I understand all of that but I have a friend who obviously has both accounts and he shows up on my Skype messenger as online using both Skype and Messenger at the same time. How is this possible? How can someone be signed into/as both at the same time?