I have some rosy-red minnows who have decided to stake out the liner folds as caves for themselves. At least I don't have to worry about dead water areas!
As you slowly fill the pond, the weight of the water will hold the liner to the bottom. Simply pull on the sides of the liner to smooth out any wrinkles, and keep working all the way around the pond as the water level comes up. The folds will practically create themselves, you just need to smooth them down neatly. Even if you don't get every last wrinkle out of the liner (and you won't), do not worry about it. As mentioned above, once the pond really starts to grow in, you won't notice the wrinkles.