The water has some bacteria in it, but for the most part, the bacteria lives and colonizes the surfaces of your tank. Glass, decorations, substrate, filter, etc. The more surface area an object has, the more room for bacteria to live. This is why filter medium and substrate are the most advised objects to move from an established tank to a new tank (they can hold a greater population of bacteria).
Doing lots of small water changes won't make any noticable changes to your bacteria population but it is worth saying that you shouldn't disturb any decorations or substrate until the tank cycles. Moving gravel around kills bacteria so hold off on the gravel vac until you are 100% cycled. Even then you have to go slow on the gravel vac (at first) because there is often a lot of garbage in your gravel that you don't want to stir up. Doing so could cause an ammonia spike.