I'd like to start a discussion on various methods for doing this. I've only done 4 myself and what I do is place the engine in its correct position, clamp it down, and scrape some coloured chalk into the holes. Then I remove it and drill away.

I don't know if this is the best method, I have made a booboo or two and I would be great to see if there is a method most people use or a tool that is quite common.