Yes, it is pretty cool. So I did as you had said, I put the flight controller on the tray behind the main gear. Do not use the jello mounts for the flight controller. use either the 3M foam that I think is 5mm thick or you can also get away with thin double sided foam tape which I think is closer to 2.5 mm thick. You can mount the GPS puck on the tail boom just behind the main frame. I had some thicker pieces of scrap plastic that I drilled a hole big enough for the tailboom and used the top as a flat spot to hold the puck.
If this is a flybarred heli, do not enable the H_FLYBAR option. It is only intended for ACRO and in my book it is not that useful. Just keep it set to zero. Then you will want to set the ATC_RAT_PIT_P, ATC_RAT_PIT_D, ATC_RAT_RLL_P, and ATC_RAT_RLL_D to zero. The flybar will provide the rate stability in the pitch and roll axes. The FF gain is the one you will have to get right so that the desired and actual pitch and roll rates match well. You could set the I gain to the same value as the FF gain but I have been setting it a little lower than that. But we can talk more about this as you get ready for first flight.
Make sure you put an RPM sensor on this so you can use the internal governor of ardupilot. You will have to tune the throttle curve initially in order to use it.
Be sure to look through the traditional helicopter wiki if you haven’t already. If you have any questions, post here and we’ll do our best to answer them.