I use 16 oz deli-cups and put 4 holes in the side with a darning needle, just below the top of the ceramic. I used to put the holes near the top edge, but find that it's more likely to allow any CO2 to 'ooze' out if it's near the top of the ceramic, so I don't even bother opening the lid for air exchange anymore. If I end up opening it to see if it needs water, then there is some air exchange, but that won't be until about 5-6 weeks into incubation, maybe longer.
If you're using the seramis, ceramic or superhatch, make sure it's drained enough so there's no water collecting at the bottom. That way you're dealing with humidity only, no direct water contact and no worries about drowning the eggs with too much water.