Do you take water from the second or third chamber? Also do you have it so that your return pump turns off during the change?
My setup is slightly different than yours as mine pulls very little at a time to not mess with my ATO. Everything in my setup keeps running while the change occurs. In your case you would have to come up with a way to turn off the return pump while the change occurs. Even something as simple as a basic plug timer will work. The best thing I can offer is do your research on what method will work best for you and implement it.
I pull from the first chamber and replace into the third myself but as I said my setup is slightly different...