I recently did entire system aftermarket in an 09 LE.
You WILL need different harnesses for the front and rear. Let crutchfield guide you there. Ask them for an extra set for the rear, because I had to cut-solder an extension for my 6x9's in rear deck. *I notified crutch about this issue*
Now, regarding door and rear 6x9 fitting. You WILL NOT be able to drop in an aftermarket 6x9 and simply plug n play. Holes won't line-up for securing to existing mounts in car, AND there WILL be depth issues/mounting issues without adapters for the install.
Try these, they will work well with most aftermarket 6x9's.
What 6x9's are ya looking at? WHat head unit did you drop in there?
http://cgi.ebay.com/ebaymotors/6x9-S...4506.m20.l1116
http://cgi.ebay.com/ebaymotors/6x9-S...4506.m20.l1116