Welcome to GenVibe!
The amp is under the front seat. You'll need to cut off the plugs and either bypass the amp or install a new amp in its place. A multimeter will be required to figure out what wire goes where. Run RCAs from the aftermarket deck to the new amp through the center console
, abandoning the existing wiring from the deck to the amp. You'll need to build a custom mount for an aftermarket amp. This video shows an amp install on a first gen base to give you some ideas. https://www.youtube.com/watch?v=X5WfkNQWI1Y
You can't run the sub without an amp. You can run the door speakers off deck power of an aftermarket deck. Replacing the aftermarket deck requires a Metra 70-2105 with the pink/red wire relocated to pin position 13, and a Scosche TA2102B dash kit. OnStar will not work at all after using this harness, except WiFi and theft tracking. Pull the MAYDAY fuse in the underhood fuse box to disable OnStar and avoid a red light on the mirror.