First, one seed per pot. Second, what you're seeing is normal. Generally you germ a seed, plant it under about 1/3 of an inch of soil and when the tap root grows down it also kinda pushes your seed up. Don't recover it with more dirt, you'd just be taking steps back. All they need now is time.

Early on you'll just have a stem sticking out of the ground with a seed casing on it. Your seedling leaves (cotyledons) will start to grow and those will push the seed off. Sometimes if the seed is just sitting on the two leaves and is no longer connected to anything I'll gently take it off using a toothpick.