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.