It does and doesnt work that way. A certain sounds loudest point is 1/4 cycle of its wave length from its origin. FOr subwoofers, this is anywhere from 9' to 2.5' SO for some of the really low sounds, you often want it in the trunk. Either way, being in an enclosed environment will help keep the sound in the car. The way to help this is to add sound deadening products that will not allow the metal of the car to radiate the sound to the outside world, and help to make it sound better inside. A power sub on the rear deck is no better then one in the trunk unless you are cutting out the rear deck. However, the custom fabrication to do this properly and attractively makes using a powered sub a lame idea as you should be using component subwoofers and amplification at that point.
If you mean to actualy put a power sub on top of the rear deck. Then that may be the single most ghetto thing I have ever heard and I may have to slap you silly. Not to mention, it will be stolen in no time.
A signel 10" subwoofer with a good amp in the trunk with a nice little box will do the trick, and do it economicly.