They stick up so as you bring your foot forward you flip the pedal and engage. If you miss it first time it means you 'might' flip the pedal backwards when you bring your foot back to try again and therefore have to lift your foot and repeat the first action again. It's a technique you quickly master, just like I've now mastered clipping in in one swift movement, whereas when I started I fumbled about trying to line it all up.
The only time it goes wrong is when you are really concentrating hard to get moving and into position and then you might miss the clip and just pedal until you have a free moment to re-clip the pedal but this equally applies to just not getting your foot clipped as you move off and having to just re-adjust once you've time to do it: Slight extra faff maybe.
Edit: Have bought double sided for my Mtn bike as that's a different situation to road riding
The only time it goes wrong is when you are really concentrating hard to get moving and into position and then you might miss the clip and just pedal until you have a free moment to re-clip the pedal but this equally applies to just not getting your foot clipped as you move off and having to just re-adjust once you've time to do it: Slight extra faff maybe.
Edit: Have bought double sided for my Mtn bike as that's a different situation to road riding