The fronts ARE 6.25" not 5.25" here is a good video walk through:

The Rear Deck 6x9s are a royal pain. You could just get med-evil on them but, most people will opt to basically gut the interior trim apart and the rear seats.
Far safer. Any ways here is a link to a text walk through with pictures.
http://2k1civic.madstatic.com/2006/0...the-rear-deck/

Good luck, order pizza because you will spend most of your day doing this wonderful job of repairing an obvious engineering over sight.