 On the top, it can even touch the seeds directly. It doesn't matter. What you're doing with that cover is you're really keeping a more humid environment for the seeds to start to germinate so they don't dry out right away. Because you can imagine that if you're just missing the top of seeds, they could dry out pretty quickly. So a cover that does allow some airflow is a great way to keep that humidity. There are some varieties that like it dark, so it will shade out the seeds.