Here is a thread in which I just answered that question: What happens to the nitrogen cycle when you switch tanks, including new substrate.
Your pet shop guy is wrong, or at least not complete in his info.
Old style, under gravel filters would grow a really substantial bacteria population on the gravel, especially when there were no plants. Plants are a great bio filter.
New filters (HOBs, canisters, sumps...) grow about 50% of the bacteria that is in the system. About 25% is in the top layer of the gravel, but not deeper. These bacteria need oxygen, and there is not enough lower down unless you are running the old UGF system. About 25% is all over the tank on surfaces including the leaves of the plants, the driftwood, the rocks and the equipment. Feel how these things have a slimy coating? That is the bio film where the bacteria live.
Nitrifying bacteria may provide less than half the ammonia removal in a well run planted tank, and a very densely planted tank can get by with just a little bacteria.
When you change substrate follow the instructions in that other post, including getting some Nitrospira 'just in case'. Do not let the pet store folks sell you something else 'just as good'. Do not waste your money.
Another way to save some bacteria is to skim the top most layer of gravel and save that in 3-4 mesh bags.
When you are setting up the new tank hang these bags in an area of good water flow. Remove the bags about one per week as long as the tests are good. This will ease the loss of the bacteria, spreading it out.