Hiya.

Atlas mapping is indeed quick. It is also very "messy". I'm not entirely sure how it determines where the model gets broken up, so I can't help you there.

My advice: use atlas mapping for non-character and relatively simplistic models that won't be too closely scrutinized. Such as trees, rocks, piles of leaves/dirt, and other 'eyecandy' type things. For characters or items that are going to get a good looking at, you're better off UV mapping them yourself with another program. Personally, I use UltimateUnwrap3D. It also has the added bonus of being a rather robust model converter, as it supports just about every format under the sun. ( http://www.unwrap3d.com/u3d/index.aspx ).