How should I transport Cannondale Bad Boy 5 INSIDE a BMW 4 Series Coupe?
None of the other answers deal with the OPs desire to keep the bike inside the car, i.e. not on a rack.

To put the bike in the car, you have to take off at least one of the wheels.

Pedro sells a "chain keeper" which is designed to keep the chain on or near the derailleur when the rear wheel is off:




This should help you considerably (along with old towels and maybe a moving blanket) to put the bike cleanly in the car with the rear wheel off.