I just installed POLK 651's in my 2006 PT and they made a real nice difference
. The location (all door mount) of the speakers on the PT probably don't help much with certain speakers I would guess (soundwise), but I had Polk's in my Dakota and put the next gen 6.5's in the PT and they sound terrific.
Buy from Crutchfield 
. Prices are competitive and they supply all you need for any installation. Putting them in my PT took about 25 minutes for all 4 (door speakers only). Crutchfield did not charge me for the wiring adapters between the speakers and stock connector for the stock speakers, as well as the mount adapter, which lays flat, so speakers do not protrude into door trim. The adapters mount the speakers real nice and easy and fit into the stock door mounts. Again - they did not charge me anything for the adapters or connectors
and all was very simple.
As far as the 6 X 9's in the rear, I had no idea those mounts were even there until I pulled the trim back to hide my Sirius antenna. I assume, as most things on these cars, the wiring is all there even though the car came without the premium sound system ? I've found they made these for the most part, with all optional harnesses installed, so they just plug in or not in production for different model PT's.
The 6X9 mounts are behind the vertical trim panels, against the back door, above the shelf. They pull away very easily and the cutouts are sitting there ready to go. What could be simpler ??? 6X9's are next for my car
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