I know this is old post but here's my 2 cents.
You can start seeds in the paper towel method and when they have tails about half an inch long and won't get lost in the clay balls (hydroton here in Canada) they go direct into the clay pellets with a little finesse; I place them about a half inch below the top of the net cup and cover with a couple balls for protection.
I've done every which way you can think off and this is the easiest and safest, the only pressure is getting the seeds root established in the first week because clay balls can dry out super fast. If your familiar with dwc you know you can mitigate this in many ways, raise water level touching the net pots, top irrigation by hand or automated, or just using a humidity dome.