This post might seem kind of specific, but I've decided its better to blog about what I'm actually doing than not blog at all. I spend most of my time on technical things in order to get to the higher level physics ideas. And this information is pretty useful.
A simple way to get atlas/blas working on mac OS X using the libraries that come with XCode is to link the headers to the "usual" place under /usr. This way you don't have to keep remembering where the header file is, and its buried deep.
sudo ln -s /System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Versions/Current/Headers/cblas.h /usr/include/cblas.h
And remember when you link to get the order right: -lcblas -latlas