Well i cant see anything in those cups but i'll just take your word for it. If you didnt plant your seeds deep enough the root will find its way by it self just dont water it too much untill it gets fully rooted into the soil. You can plant your seeds as deep as 4 inches though without worrying about them not coming up. You know that they cant stay in those cups the whole time their growing your going to have to transplant them into larger pots later when they start to need more space for their roots. Unless your going to harvest them when they are still realy small. Also make sure you have holes in the bottem of those cups for drainage looks like you have that with the trays under them. Your lights don't look to close at all if anything i would put them closer but it depends what kind of lights your using. You should get them on a watering cycle that your plants can get used to like every few days youll know when to water them again when the top inch or so of soil is dryed out.