It may be a good idea to consider raising the alkalinity in your aquarium water. Like other have mentioned, there will be a ph shift with CO2 injection, but you don't want to bottom out your ph into the 5's just because a pH shift exists; if you increase your pH when the CO2 injection is off, then the lowest value you dip to will be higher (i.e. 6.6 pH instead of 5.6).
If you are interested in this, you could slowly increase the KH of your water change water and over several weeks manipulate the chemistry in your aquarium. All that matters here is if you are comfortable with bottom level of your pH.