Use the AmpPro, this keeps your center channel information and lets you control the volume of chimes so you don't miss the center channel and also gives you a flat digital signal. All of the factory EQ and DSP are in the OEM Amplifier so by using the AmpPro you get the original signal before all of that... This also means that you won't HAVE to disconnect the center channel and factory sub as you 'could' run them in parallel with the new JL equipment but that would likely cause all kinds of problems with Time Alignment and Phasing so the best suggestion is to disconnect them at the driver.
Yes, people have run coaxials and tweeters in the sails or pillars at the same time but it's a HUGE No No. Running multiple drivers of the same size and frequency range on the same channel causes comb filtering and that's nasty. Just don't.
The midbass in the rear door and the wideband in the D-Pillar is the about the dumbest idea that Jeep has ever had and if you want to simplify the system, then coaxials in the rear doors is a simple solution but it always irks me to have speaker grills with no sound coming from them and people asking why so I use the widebands in mine for the bulk of the sound and the midbass door speakers are bandpassed and reduced in output to the point that no one but the person sitting by that door can even tell they are there. More on the D-Pillars in a moment.
Audiofrog is a HUGE jump from JL C1 components and there are a whole bunch of drivers in between that you should consider before simply using C1 for the name. In fact, before going with C1 components, I would suggest that you install the AmpPro and the amplifier on the factory components first and see what it sounds like without all the factory filters and EQ, you will be amazed at how good they can sound with a proper tune and source.
Where are you planning to mount the amp if not in the tire well? The factory amp is in the left rear quarter and you have to remove the load floor and spare tire surround to get to it but once you do you can get a T-Harness to use the factory wiring and not have to pull all new wire through the vehicle. This also lets you return to OEM if you decide to sell down the road. 12 gauge wire is fine for the Sub.
Flush mounting the tweeters in the sail is easy, you pop out the oem grill and then modify the opening to fit the tweeter you buy, the rear D-Pillar is not as easy. The wideband that's in there is a 3.5" and you need skills to modify an opening that big to fit a small tweeter but if you've got the skills then go for it but you really should try just doing the Amp and Sub 1st to see what you've got... I think you'll be surprised.
My suggestion for mounting Subs in the rear cargo area is to do it in some way so that it can be removed easily (like the twist clamps on road boxes for touring gear) but velcro won't do and using ratchet straps would be more secure. Bolting it down to the false load floor is also problematic as it makes removing the load floor to get to the spare almost impossible for one person. But at least bolting it down is safe.
Flex tubing or any other tubing won't change interference. You only need to run power from the passenger seat to Amp mounting location. Then, Fiber Optic from the AmpPro in the dash to the JL Amp and speaker wire from the JL Amp to the OEM Amp so interference should not be an issue. Use 1/0 OFC Copper Welding Cable for the power and any reputable OFC Speaker Cable.
Deadening: once you get the door cards off you are going to see a huge plastic assembly that's fairly well sealed off to the metal door (compared to the designs of the past) but don't be fooled, to get that panel off you have to remove the window glass 1st and it is not for the faint of heart. Once you do, deadening inside the door is much easier than the previous designs and this is not where you want to skimp out. The investment you put in deadening and doing it right the 1st time will be the most cost effective improvement you make...