Where and What Size Hole?

I Absolutely agree with Demonracer leave the original hood untouched.

You can also order a fiberglass hood with the scoop already installed and save yourself a lot of labor. They will put it in the correct spot if you are going to use a stock transmission mount location. The stock location is known and the transmission and engine length is known and so they can put the hole in a place that will work even if it is not perfect match to your setup. I am assuming you will be using a hood scoop of course.

If you are not going to use a hood scoop, then Professor Fate has the best process regardless of metal or fiberglass hood because the edge of the hole will be exposed. And you will just have to wait to get the car back from the shop.