When I took a sheet metal course he instructor was anal (with good reason) about drilling holes perpendicular to the material. His trick was to use the reflection of the drill as a guide. The two pix shows what a drill looks like when at an angle and when perpendicular. If you keep this in mind when drilling, it becomes automatic after a while.
Dill is at an angle 
Drill is square to surface
The same technique is even more important when riveting – especially skins. The rivet gun reflection will tell you when you are square with the surface and will help prevent smileys.