You can't neutralize calcium carbonate. Acid will dissolve it, so you can wash it out, but if there is any calcium carbonate left it will continue to slowly dissolve in the water and raise the GH and KH. If you plan to use an estimative index dosing method, which requires regular big water changes, a small amount of calcium carbonate won't be a problem. The water changes will keep the amount in the water to a minimum. It is when you only add make up water, over a long period of time, that the KH buildup could become a problem for you.