Yes, I cover it back over. I've never bothered with positioning the seed with the tap root down, it knows how to grow
. I don't bother with lights until the seedling sprouts, and then I either stick it in a back corner of my veg room or put a 23w CFL over it about 3-4 inches away. I don't put too much light on the seedling for the first day or so, and even then I take it slow with lighting, putting the seedling farther away from my lights than I would a much more mature plant. You just have to figure out what the little seedling can handle without stretching. For me its 3-4" from the 23w CFL or 12" or so from my 150w CMH.