Welcome to the forum.
The speakers behind the seats... are they in the rear storage compartment, or are they seperates, aftermarket, speakers?
Not sure if this was a standard config from the factory.
The cup holder has been covered.
I plan to put a 6" plus display radio in.
Your questions...
Is this a standard config that I'm starting with? I don't see the/a storage cubby. I believe someone may have moved the temperature control unit from the top to the bottom.
Can you move the temp control up and blank out the bottom with a bin? I believe most people, when installing a ~6whatever inch AV stereo setup will go double din. Pull out the cup holder and the existing sound unit... in goes the 6" display you have.
Pull the CD holder and tuck in the aforementioned, yet now absent, storage cubby.
Lets see some pics of the car.
Should I keep the external amp to drive the rear speakers? I would say yes if those rear speakers are OEM to the storage compartment. Someone who has knowledge of the sound system setups may contribute to this thread.