There was a great thread on RC a few months ago but sadly all the images disappeared and it became somewhat useless...
I'm going to take a detailed photo log when I redo my refugium and set up a website for stuff like that.. Until then, what follows is a crappy narrative explaining it:
Track the exact hole you want to make.. Couple ways to go about it.. One way is just to stick your bulkhead onto the tank and trace around it with a marker and then when you drill the tank, make sure you're grinding away on the INSIDE of the circle you drew. Another way is to use a compass. I won't go into the nerdy details of how I did it with the compass.
Get ye your tank out back (ideally). Turn ye garden hose on and keep a constant flow of water over the site you're drilling (not a torrent, you just need the diamond bit to remain wet or you'll wreck it). Some folk just use a spray bottle to keep it damp but I'm a little leery about so little water.
Initially, you want to make a pretty chubby hole to get the bit down and through the glass. This is really the only dangerous moment - if you were to plunge straight down, you could get through the glass fast, but what happens if you were you twist the Dremel tool just then? You'd have no room for error, and you've essentially have a very strong lever through the glass and end up breaking the pane.
To mitigate the risk of that, do a very lazy hole initially. Remember when you were just learning to write and you were very conscientious about dotting your 'i's? Instead of a lazy man's dot, you did a little swirly dot, didn't you? Do that through the glass. The hole you're boring will end up being about twice the size of the bit, but it only takes a few seconds longer and guarantees nothing stupid happens.
Once you're through, the fun begins. I will say this in bold, but you will probably still be hesitant like I was my first time:
You can push pretty hard with that Dremel! The first hole I drilled in a 10 gallon tank (3mm glass) took me about 45 minutes, maybe even an hour. Now when I did the 20 gallon tanks in the store (5mm glass), holes that were even bigger than my 10 gallon took about 4 minutes each. As you grind your way along, you need to make sure the bit remains wet - that's the only criterion for success. To get the cut going faster, I suggest "sawing" the Dremel up and down.. The varying thickness of the bit makes pretty quick work of the glass.