Interesting. So are you just updating the atlas sprites rect directly to animate it? Rather than creating an animation action based on frames (the default cocos2d way)? I didn't get round to trying that.
For the project I did this on, it consisted of a characters head, around a 3rd the size of the screen. Instead of animating head/eye/mouth movements based on full frames of the head being updated, we imported the head, hair, mouths, eyes all separately and recreated the animations within cocos2d, or in some cases ran atlas based animations just on these smaller AtlasSprites.
That approach may or may not work for you depending on how complex the sequences are.
The other main reason we opted for this method was due to the very large number of animations we required, we quickly started to get a large number of textures needing to be loaded, & so the app size, and texture memory requirements were ballooning quickly.
We were also about to run into the issue you've got, of requiring multiple atlas managers to be used on a single animation, and so would have needed to write something to handle that.
But we had a very particular requirement (& a want to keep under the 10MB 3G download restriction). You may be better off writing some sort of wrapper to toggle between different atlas managers in your case.