One of the biggest things is that you need to make sure the ground strap is firmly grounded to the chassis of the new head unit. Also, the sub receives signal from both the front and rear speaker outputs from the head unit. This won't be an issue if you are just upgrading the head unit and you aren't using an external amp because you will be just attaching to the original wiring. If you are using an external amp, you will either have to run the factory speaker wires to the amp or find the point of connection where the sub receives its signal.
the adapter harness for Chrysler does not label the wire for the sub power signal. If memory serves, the wire labeled "power antenna" is used as the power signal to the sub's amp. The sound itself is channeled through the harness from the factory amp and the HU, but I bet you're missing the 12v feed like I was.
I have the stock sub driving a rockford 6 3/4 sub just fine. You gotta hook the remote lead from the aftermarket HU to the power antenna lead of the chrysler harness adapter to make it work. Now I just need to eliminate that rattle in teh soundbar from the new pioneers.