I recently changed my substrate from pebbles to black sand/small rocks. I removed all the pebbles from the tank, which took me a while, and I did it over two weeks removing it at each water change.
I then got the new substrate, and half filled a bucket. Washed it and then using a pvc pipe I added it to the tank. The pvc pipe helped to put in on the bottom of the tank and of it was still a bit dirty did not spread it all over the tank. I did this over two days, as it took a while to clean the new substrate.