You should get the manga. The entire third (and most important-that-explains-everything) storyline was taken out of the anime, because the anime ran into the manga,as it happens sometimes. It was made into Samurai X, but SX is alot more serious and doesn't have the same feel as the original. (Since, after all, isn't made by the same people) The third part of the anime, although pretty fun, is filler made by the anime production team, and not based on the manga. It's still okay however. You just miss out on alot of explanatory stuff.

So...get the manga.

Edit: You can watch the anime on YouTube, if you're patient enough