Too many fans can create too much turbulence and actually raise temps. There was a famous experiment with a mega-fans case that took the idea to the extreme and proved it.

However, to answer your question, generally in at the front and side, out at the rear. Think of the overall airflow path your fans will create, try and get the components that need cooling in that path (hdds, gpu, cpu, psu), and if you can see that some fans will be interfering with one another, think about making baffles with cardboard, foamcore, or plastic and tape.