You need a pocket to fit under the aftermarket radio to make up the difference in size from your aftermarket and factory. The factory is double din and most likely you are putting in a single din. And yes you need that harness.
Yours might have an amp in it as well, but its the easiest amp in the world to bypass. If it has an amp it is below the radio and is a little silver box. There will also be a plug running from the factory radio to this box. If it is there, remove the 2 screws holding it in and pull it out. There are 2 plugs going into the bottom of it; these are your standard toyota harnesses.
After that its pretty simple. Make sure to hook up the power antenna wire though!