The majority of the beneficial bacteria live in your filter, so doing water changes won't disturb it, unless you don't dechlorinate your water.
You should test your water, or at least have your LFS test it for you.
If the water is looking dirty after two days, even if you are overfeeding, you really need to examine your filtration. If you're not sure that you have enough for the stock you have, you can list for us the fish and their sizes, the filtration, and size of the tank, and what you're feeding/how often, and we can give you some ideas.