In the first few set ups I did have it run at the base of the car. I found that there was no real improvement one way or another. All it did was add more tubing and weight. In my many prototypes, right were those ram air inlets are is the most optimal spots. It is dangerously close to were the best PSI flow is, on top of the cool air just flowing right into it.
Those AEM bypasses that you mentioned, I haven't really come across. They sound really cool, I'm totally going to look into those tonight.