You have to give it at least 12 hours to make an accurate record, I think. I did mine over closer to 24 hours to really get a real-world number that includes time on a bedside table and the full day's worth of different use.
Basically you start by clicking when the second hand gets to 12, and then just wear the watch normally. Come back whenever is convenient after 12 hours, and click again. Just make sure to double check the minute hand is also accurate. The first time I tested my Squale, it came back as +60.6 seconds when it was actually only 0.6 seconds fast, but once you accept the test, you can't modify it.