Adding an RKE module is not going to help you with that. You need the existing system fully functional in order to make an aftermarket RKE work.

It all starts with the SKREEM.
The driver door lock cylinder AND the FOB both cause the SKREEM to send a lock signal to the Body Control Module (BCM). The BCM sends messages on CAN BUS B to the CLP/SSM telling it to "lock all locks and set the alarm". When you hit "unlock" or turn the cylinder to "unlock", the message sent is: "Unlock and unset the alarm".

If you hit the lock button on the console, the BCM tells the CLP/SSM: "Lock the doors, but don't set the alarm".

You must use the SKREEM to manage this unless you can decode how the interactions between the SKREEM and BCM work at point "B" in the diagram. You can find these connections in the service manual, it does not look that hard, but I'm not going to disturb these connections in my car to find out, if you do,please come back and tell us how it works.

But unless you are REALLY GOOD with CAN BUS communications (and I sure as hell am not), you cannot directly talk to the CLP/SSM.