Turn off any air pumps, unless they are the only filtration. If this the case, check the pump for an air filter. If there is one, replace it with a new one, preferably one with carbon. If you're running a UGF with it, replace the tube filters with new ones that have fresh carbon.
Cover the tank with a large sheet when you're actually painting. Make sure there is adequate ventilation throughout the process, and at least 2 days after completion.
This is probably overkill, but safer. I recently painted my bedroom and bathroom, and didn't worry about my tanks, but they are one floor away from where I was painting, and I don't use an air pump for anything. I did cover my tank when the patio door right next to it was replaced, to keep the dust out. Didn't have any problems.