The connectors on the ends of the bypass harness are different from one another and will only go one way. This is because the input side of the factory amp connector has the power wire to the amp but the output side only has the speaker-out wires. It IS as simple as disconnecting the two connectors from the amp and plugging the wiring bypass harness into them.
Like Ru Dawg said, though, the hardest part will be getting to it. In addition to the press-pins around the side window, you will have to pull back the carpet from the trim panel and remove three or four screws that go into the floorboard, remove the seat belt hanger (T-50 Torx bit), remove the two phillips screws from the rear side door scuff plate, and remove the floor scuff plate that goes across the back edge of the carpet. All of this should allow you to easily fold the panel back enough to easily access the amp. To completely remove the panel, you also will have to remove the coat hook above the rear passenger door and the passenger door scuff plate.
Good luck