Having read the first 12 volumes of the FY manga myself, I have to say that it's been trully a memorable story to read. I actually loved the character designs in the manga a whole lot and it seemed like Yuu Watase spent so much time on them. The anime character designs were so good too. They were both so well done and so beautiful.
As far as differences go, I thought Miaka seemed alot more realisitic in the manga. In the beginning of the story, it seemed like there was more character development with Miaka's home life much more so than it showed in the anime, but other than that, there are only minor changes in differences from the manga to the anime. With that said, both the manga and the anime are excellent, and I'm sure you'll enjoy them very much if your into either manga or anime. I would highly recommend you getting the Fushigi Yuugi anime and getting the rest of the FY manga as well, you'll definitely like both of them very much.