it seems to be a matter of preference, I know people who seal them up and open them once a week or so to allow air exchange and others who add a small hole or two to allow some ventilation during the whole process. If you can keep the humidity way up there for the duration it becomes a choice on which method you prefer.
I personally use the 9.75" wide deli tubs (3" high or 5" high) with the pre-punched holes. I cover 10 out of the 12 with electrical tape for the duration of incubation, then in the last couple of weeks, when they start producing additional heat at that stage of development, I open an additional hole (or two) as needed. It works great for me so that's how I will continue to do it! Find what works best for you and go with it!!