I believe you made a good chioce with the alpine and eclipse combo. I would strongly suggest running the in line filter from the deck even if the deck puts out a strong enough signal (so they say), the sound differnce should be noticable and they are not expensive. As for the 6.5" in the rear i thought the same thing until i pulled the panel off the 6.5" will be better in the over all sound quality. As for factory speakers the differnce compared to aftermarket is great. The cone material and tweeter asssembly in an aftermarket speaker was designed with listener in mind unlike the factory mass production theory. As for my truck im running infinity 6002i 6.5' in the doors, a mtx 404 200 w rms 4 ch, 2 mtx 1501d (1500w 2ohm) and 2 eclipse 12 alum. ikept my factory deck and tweeters connected and opted for the inline filter. i have one of the loudest trucks in the area. for installation ideas try www.sounddomain.com theres some cool rx installs their.