First, the person/persons at the LFS are idiots. There are no (or only a miniscule amount) good bacteria in the water so the LFS has told you trash (not a big shock). The bacteria attach to the decor and walls of the tank but mainly to the filter media where the most food (ammonia and nitrite) pass by. Therefore the vast majority of the beneficail bacteria are in the filter. When people talk about cycling a tank, technically, you are cycling the filter.
Also, you have to test daily so you know what your tank is doing. Testing and changing water once a week in a cycling tank equals dead fish, hence, they get to sell you more. Water changes are mandatory in a cycling tank to keep the toxins (ammonia and nitrite) at levels that won't harm the fish. You really want to keep the levels at or below about .25 ppm. And contrary to popular belief, the tank won't cycle faster with high levels of ammonia. The lower the levels are kept, the quicker it will cycle.
Now for the rocks. If that is all you added to the tank, then it's probably what caused the rise. Simply put a drop or 2 of vinegar on them. if they fizz and bubble, then they will raise your pH.