There is a very simple trick to figuring out how deeply to plant seeds, whether you're sowing them in flats or pots indoors or out in your garden. Here it is:
Seeds should be planted at a depth of three times the thickness of the seed.
So, for example, if you've got a morning glory seed that's about 1/4 of an inch thick, it should be planted around 3/4 of an inch deep. Large bean seeds that can be 1/2 inch thick or more may need to be planted 1 and 1/2 to two inches deep.
For very tiny seeds, place them on the surface of the soil and barely cover with soil or vermiculite. For seeds that need light to germinate, simply place them on the surface of the soil and press them gently to ensure good contact with the soil.