Someone mentioned to me that AMD systems utilize better ATI cards better and Intel systems run Nvidia cards better. I was wondering if this was true, or even significant, as I am planning on building a new computer soon.
I am not sure where someone gave you that idea. If that were the case, just think about how many people owning AMD systems wont buy the GTX460. Which in turn would be loss of business of either nVidia/Intel/AMD/ATI, whichever parties are involved.
So CPU and GPU have no correlation and are perfectly independent in their working and you can have any combination you want.