I have a 2009 Flex and recently something under the dash behind the radio has started clicking loudly when i turn the heat on. It sounds like a relay or something but I'm just not sure. There is also a clicking sound from the back when i turn the A/C on in the rear of the vehicle. Any help will be greatly appreciated.

 

From your description it sounds like it could be a blend door activator problem.I believe FordTechMakuloco has a video on U Tube describing the sound and how to check and correct it.