Well I have never worked on an 08, but I am familiar with Chrysler Infinity systems. If you have a factory amplifier for your regular speakers as you indicate, the swap to an aftermarket head unit will not be easy.
I have a Sebring with the infinity system. The way it works is, the head unit provides un-amplified signal to the amp. In my case, it is under the seat. With an aftermarket head unit, typically there is a built in amplifier in the back, as well as RCA pre-amp outputs. Now normally you would have the option to either power speakers directly from your head unit using the built in amp, or use an external amplifier to power the speakers.
The thing is, you can not amplify and amplified signal. I mean you can but for the purposes of car audio, its not going to work, and your going to fry your amp in the process. So, if your infinity system uses an external amplifier like mine does to power your DOOR speakers, you will either need to re-wire your jeep's system so that the speaker leads go to the back of the head unit (a big pain) and bypass the factory amp, or replace the factory amp with an aftermarket amp that has RCA pre-amp inputs. At this point, you would merely run a couple RCA signal cables from the back of the aftermarket head unit to your new aftermarket amp.
Im fairly certain all the shop did was use a line output converter and tap into a speaker lead to get your sub woofer signals. If you replace the head unit, you can run an RCA cable from the aftermarket head unit directly to your sub amp for even higher sound quality.
You will have an increase in sound quality if you switch to a QUALITY aftermarket head unit (im talking about eclipse, alpine, and higher end kenwood. That means no JVC, clarion, dual etc etc). Keep in mind though, the best sound quality comes from using your aftermarket head unit for signal only and using an aftermarket amplifier to drive your speakers.
I would say at the very least, replace your speakers. OEM speakers are usually crappy paper speakers and you will notice quite a difference in sound quality by going aftermarket. I have JL TR series in my car, and they sound excellent, crystal clear. Keep in mind your factory amp, as well as the amp in an aftermarket head unit is limited in power, so decide what you want to do as far as the head unit goes before buying speakers. If you have limited power, you dont want to go buying high end components. If you use an aftermarket amp and you have some nice power to play around with, you can consider components.
Jim