Hey Bleedingthought!
Well today my fish club and I drilled three holes in two tanks. Both tanks were top/open side up and I drilled them on the back glass. Our reef club will have a video posted on the website hopefully sometime soon. Ohh great... now everyone gets to see me sweat it out in front of a crowd drilling a pair of tanks.
I find it just as easy to drill the tank laying on its side or standing upright. Although I will admit that it does help to have someone watching from the side to tell you if you are working directly in or if you have the drill angled up or down. It is difficult to tell sometimes when you are holding the drill exactly how perpendicular you are to the tank surface.
We will post a link so that people can see the video tutorial on tank drilling.