Is space limited? Is there a reason you don't want having separate subs?
Will you be able to place the 2 subwoofers on opposite sides of the room (front Center + rear Center) ?
Where can you place your 2 subwoofers? Only on either sides of the front wall? If this is the case, then it's the same location as having subs inside your front towers.
Dedicated subs, however, usually have more bass output. How much bass output do you want?
There are a lot of variables, including budget, space, and aesthetic. Do you want amps to be OUTSIDE of the subs and speakers? Have you thought about what you would do if the amps inside the speakers or subs fail?