There is no sub in a commander.
There is only one AMP in the Commander, it is a 4 channel under the middle row seats. It is also integrated in the system for the car.
If the installer in not wiring up a full install and just trying to splice together your new sound system, I would walk away.
The RER radios sells for around $450 on Ebay... Just the unit. (which you can just plug in and it will work by the way)
You have to get a MYGIG adapter in addition to the radio, to enable useful functions like being able to use nav while driving and watching movies while driving.
Chrysler was super smart when they went with the MYGIG family of radios, the system is integrated with the brain of the car and not easily replaced with aftermarket. VW and Porsche, along with a couple of other makers went with this also in order to lock up their customers from tampering with their designs.
As long as you are happy with your wire looms getting chopped up, I would wait and save up for buying a factory radio. It is not like the factory stuff is crap either, do not believe any hype that any other brand is going to outperform the factory head unit.
'06 Hemi Limited 4X4, 6(ish)" lift, 35" General Red Letter, 1.25" spacers, Mopar CAI, RER and mygig lockpick, blue Interior LEDs, stub antenna 3", Callahan Red Brake set, 6.1L SRT8 exaust headers, full custom 3" exhaust from headers back, Fastman 847 ported TB, BBK Fuel Rails, 6.1L injectors, JBA UCAs.
Coming soon: Nitro gear 4:10, 50" LED bar, catch can, SA hidden front winch mount, 4XGuard brush guard, Stage 2 Mopar kit for 5.7L.