Yeah, the anime is great, and I had a hard time with figuring out what was going on as well. xD But it all peices together in the end.
Er.. well actually, the anime leaves out a LOT, and by a lot I mean as much as a character, in the anime they're in one episode, and doesn't really get to know anyone, but in the manga they're much bigger, and they stay around longer. *-*
But if you ever consider watching it, or reading the manga and need help understanding anything you can ask me. =D
I'm in the progress (a very slow one, because I was all into AnC until I saw .hack//SIGN, and since then been on a .hack craze and haven't had time for my AnC sites XD) of a site for AnC, revolving around the whole series, wiff piccus and everything.

I also have a growing shrine to Aki. I luuurve Aki. XD;
But yeah, AnC blew me away.

It's such a depressing anime deeper into the series. Getting near the end, last 6 - 8 episodes it gets so darn sad XD