I am not sure I know just what you are asking. Are you talking about seeds or are you referring to rootlets? Let's go with seed, are we talking stratified seed or green seed? If you are planting seed (either one) it will need to be covered. You do not want the seeds to dry out or they are ruined. Keep in mind how nature plants the seed. They fall on the ground or leaves, then this years leaves will fall on them to cover them and both layers of leaves will act like a mulch to help keep the seeds moist- not wet- just moist, in most cases. Now if you are planting stratified seeds, they should germinate in the spring into tiny sprouts. If you are planting green seeds (ones pulled from the plant this year), they will not germinate until the spring of 2010.
There is a lot of variance on what people say for planting depth. I have heard anything from just on the top of the soil and under the leaves, to one inch deep into the soil and still under the leaves. I believe nature puts it on the ground and covers it with leaves.
If you are trying to stratify seeds in a layered box set up, you will need to keep them moist, not drenched, just moist. It is when they get dried out that they die. Hope this helps. DR