The Secrets are... complicated. The easiest way to describe them is as a fusion of science and belief made into something real. Scientists discovered the First and Second secrets, but if humanity hadn't believed that there was more out there, we might not have ever found a way to unlock them. The First Secret gave a means to move through space-time in a way that had never even been imagined before, a method that remains the Shiplords' primary means of FTL travel. It worked in defiance of physics, and in defiance of every theory that said its energy cost should be higher than the annual power output of earth.
Actually understanding what the Secrets are beyond what they do is something that Insight isn't even sure that the Shiplords know. It's certainly beyond humanity right now. What they can do, however, is incredible. The First Secret gave humanity the stars - or would have without the Shiplords being what they are. The Second gave you genetic engineering on a truly incredible scale. The Dragons were a product of this, but because of how they were made they weren't automatons. You made protectors, but in doing so extended the family of humanity. No, before you ask, the Dragons weren't once humans. But you made sentient beings, living things with a powerful protective instinct keyed to humanity, and engineered as much in the way of power into them as you could.
The Secrets are numbered by all who discover them, and as far as Project Insight was able to find, the First Secret is always the First Secret, the Second is always the Second, and so on and so forth. This does not, however, mean that they are always discovered in order.