I added two 12's to my Sonata and left factory sub mounted but disconnected the wires. I'm not sure opening that 8" hole would make much of a difference or not. You could certainly try it both ways to see which sounds better to you, but I'll warn you that it's not a quick process to remove the factory sub - you'll need to take the whole rear of the car apart.
I added a 15" sub, left the oem in place, when I really wanna let the bass in, I fold down both rear seats. I usually have the driver's side down all the time. I have toyed with cutting the seat behind the center armrest for the times when the seats have to be up.