I just did that too! Great improvement! I have 6.5" Alpines in the door, some 3.5" Infinity's in the dash that fit right in after taking out the bracket and cutting off the part under the cover that sat on top of the old ones, unplugged the worthless things in the headliner and this in the back:
I was thinking of going with that same exact box and sub... I agree on the ceiling speakers.. Not sure what I'm going to do about that... I put 4in speakers in the dash. They didn't fit in the mount but I got them in there.