can i use my thunderbolt in built isight camera with Skype?

recently bought the 27" thunderbolt which is hooked up to my new mac pro 13". If I have my mac closed and i'm running off the monitor and I skype, the inbuilt camera doesn't work. I have to open my mac up and use the one on that instead. Anyone else had this problem?

I used it for facetime the other day and that worked find so I know the camera itself works.