2 little holes isn't going to allow for much air to flow through, meaning your cooling would be very inefficient. If you take the case apart, you can drill as many holes as you want, but I would mimic it after an actual cooling slot (A large area with slots or tens of holes) to allow the cooler to get air into it.
You might also find that although you are blowing air into it, you need a place for that air to exit as well, or it just builds inside the case, not doing any good.