how do you not enjoy it!? :O
and it kinda sounds like you watched a episode from both, because the original is very flowing, like it all falls in with eachother, and the story makes sense....
brotherhood is the second series; its based on and follows the manga.
I think I understand where your confusion came from. The first episode in Brotherhood (the 2009, thus second version of the series, anime) is pretty much a self-contained episode, but at one point, Ed and Al are on a rooftop, and talk about how they had train tickets to Liore and have to postpone that trip. The second episode is after Ed has got out of the hospital and they are headed to Liore, and they talk about what Ed is hoping to find there, which then leads into several flashbacks about why they want the Philosopher's Stone. It has some voiceover monologue from Ed and loosely covers their childhood, how they came to attempt Human Transmutation, and what resulted.
After that, it dives back into action, with the Liore story, and so on. If you want to give it another try, please do. If not, I'm sure you'll find something you'll like out there.