Welcome,
Traditional Helicopters have been gaining more and more support within ArduPilot so you came in at the right time.
I would urge you to check the excellent tutorials that @ChrisOlson has published here http://ardupilot.org/copter/docs/traditional-helicopter-configuration.html
and also follow our progress on bringing a new 700 class heli (a ThunderTiger E700) to the newest firmware available (3.6RC), which has already given some great results. Here Thunder Tiger E700 and here ThunderTiger E700 v2 - Going electric
About positioning the Flight controller is not critical, as long you are careful with vibration isolation, or use a Flight Controller that provides some isolation internally.