Where does the flow of power come from for a Transmutation Circle to work?
Yes, It's different. The original FMA anime didn't wait around for the manga to catch up (like DBZ did), so it diverged instead.  

What you ended up with was 2 completely different endings, and 2 different explanations for why alchemy works:


In the original anime, the explanation was that It came from the other side of the gate.
In the manga and in brotherhood, it came from energy that was already in the earth.