I would not recommend retaining the factory deck. I can speak only from my experience with the single-disc CD player that's in my 03 LX Coupe 4 Cylinder. I installed a nice Rockford Fosgate amplifier and a single JL 12 W3 sub. I tapped into the rear speaker wires and used the line-level inputs on the amplifier. The stock CD player didn't produce a clean enough signal to be amplified, and my amplifier was amplifying distortion. There wasn't as much bass as a 12W3 should have been producing, and the sound quality was very poor.
I returned the amp and donated the sub to my brother's 90 Civic Hatchback. I still have the power line running to the back of my car, and I'm waiting for someone to release an in-dash install kit for an aftermarket deck in the 4-cyl. LX Coupe. Since my stereo doesn't have any climate controls built in, I have no need to retain the factory deck. The idea of having a second (functional) headunit replacing the center dash storage compartment seems crazy, though there are two nice things about it:
1. An aftermarket headunit in the slot where the factory headunit is located wouldn't match the design of the dashboard.
2. An afternmarket headunit in the slot where the factory headunit is located would stand out like a sore thumb, and having an aftermarket unit hidden below the AC controls might be a better theft deterrent.
Anyone have any pics of an aftermarket headunit installed in their 03 Accord?