the extra plugs on the back of the standard head unit are for things like mini-disc and cd changer.
all you need to do is plug in the iso adapter.
the best cable to use for sub remote os on the iso adapter itself, is the remote arial one, i think its brown, also you will want to put the handbrake cable of the pioneer loom to earth rather than faffing about fixing it to your handbrake.
I have the 3200BT and it is a fantastic piece of kit, and as has been said, the only difference is app mode.
If anyone is interested in the 3300bt i can see what kind of deals i can do with my good friends who own a car electronics business.