I haven't noticed, is Battle of Atom crossing through all of the X-Books or just Uncanny and All-New?
It's all the X-Books. That's one of the main reasons I started collection all the issues for 'Battle of the Atom' because I was collecting Wood's "X-Men" and didn't want to be left out of the main storyline.
Despite Bendis' recent Uncanny X-Men (and yes, it was quite a mess), this is one title that I will be keeping after "Battle of the Atom" is over. I've heard some bad things about it, but Magik is one of my favorite characters, so I'll be staying with it for as long as it entertains me.