You shouldn't watch either as they are both terrible, but for your question FMA and Brotherhood are essentially different series. From the Wikipedia article, "Unlike the first anime, which had its own original story, the second series follows the story of the manga."
I watched Puella Magi Madoka Magica over the weekend and was highly unimpressed by the show. The characters were boring and the plot was stupid, especially when the explanation for why the magic girls were created comes around. Typical overhyped crap that people wet themselves over because of some apparent mindforget factor to the story. Though bad, the plot was easy to follow and there was no mindforgetery.