water changes, done correctly, are only good for the tank. they won't hurt your fish or your filtration. make sure to always add dechlor when you fill the tank (before you turn your filters back on) and try to keep the temps within a few degrees of each other. a lot of people do 50% changes every week.
if you are replacing water with a bucket, then treat the amount of water in the bucket before it goes into the tank. if you are using a python, then add the dechlor before or while you are adding the new water, and treat the entire tank volume.
so, if you're using a 5g bucket, you add 1/2ml prime to the bucket, then put the water into the tank. repeat for every bucket.
if you use a python, and you have a 50g tank for example, then put in enough prime for 50g before you add new water through the hose.
if chlorinated water is kept separate from tank water, there is no need to use enough prime to treat the whole tank. if you read the instructions, it says what to do on the bottle, i believe.