There is an adaptor plate that the stock amp attaches to. The metal adaptor plate slides into the two mounts just above the spare. There are two tabs on top of the adaptor plate that are bent 90 degrees towards the back of the car. A bolt goes into each tab that hold it to the fire wall. There are rubber covered nuts, sort of an anti-shock mount, that these bolts go into. I got new rubber nuts from the stealership $10.00 each. Be careful and don't over tighten the bolts that go into these nuts, go easy.
The thumping you hear from the door speakers is one of the main reasons people swap out the Becker head unit. There is a crossover in the Becker unit and this thumping is the stock sound.
If the aftermarket speakers look stock, then I wouldn't go through the effort of swapping them back to stock, but that is just my opinion.
