To mount anything deeper than the stock speakers, you will have to cut out the plastic molding basket in the door. However, if you go too deep you'll interfere with the window. I have Boston Accoustic speakers in my car, and I have about a quarter of an inch clearance between the magnet and the window gears.

Also, since you are replacing the factory head unit, you will need to bypass the rear stock amp (has to do with the Accoustic Feedback garbage). It's a little black box mounted under the rear deck between the rear speakers (close to the seatback lock release).