I have read lots on drilling perpendicular holes using a pair of squares, but I only have one small one. Two squares would allow you to check for square in both directions without moving your head, which is certainly preferable (as shown in this video by Shannon Rogers).
With one square, you can line the bit up with the square’s edge looking from the side:
And at the same time you can prevent any side-to-side variation by looking though the square at the bit:
Once the drill is 1/2″ or so into the wood, it is self-jigged and keeps going in the direction it started.
I’ve found that once I have drilled four or five holes, my body figured out the correct stance and perpendicular-enough holes could then be drilled by memory.
T r i a l & E r r o r 
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There’s an old trick and a jig that Noah must have used – takes all the guess work out and it’s minutes to make……..
If you do a lot of draw-bore joints or holes that need perfect alignment, this jig is ideal.
– Take a piece of 3 x 2 or similar about 6 inches long.
– Cut one end dead square all round.
– Mark two lines at 45 deg from each corner so that they meet in the middle. Do this on both sides.
– Cut along each line to form a Vee shape that is at right angles to the sides.
If you mark the position of the hole and centre your drill bit on the mark, move the Vee section up to the drill – clamp it if necessary – and you should now have a vertical drill.
Here’s a blog that explains it:
http://www.theenglishwoodworker.com/?p=309
All best from Wales
Reblogged this on The Woodwork Geek and commented:
Here’s a simple way of drilling straight holes with a brace, though it should also work for eggbeater and powered drills as well