I am not too familiar with root riots. Are they similar to rapid rooters? I personally love the paper towel method. I now mix up several drops of rhizotonic root stimulant with the water that wets the paper towels. I am on my first grow at the moment, and when I was germinating my seeds I did it 3 different ways with different seeds to see which worked the best. The rockwool completely and utterly sucked. I dont think any of the 15 seeds in that one would have been viable for a plant. The other 2 things I did were both paper towels (shop towels with no dye or fragrance) and ziplocs. The only difference between those two was one had ph balanced water with rhizotonic and one just had ph balanced water. 10 seeds in each. Both ziplocs were placed in the pantry where its warmer and darker. 24 hours later the bag with rhizotonic showed much better results than the one without. At 48 hours the rhizotonic bag seeds had taproots around 2 inches where the other bag had maybe 3/4" taproots. After that I put them in rapid rooters within hydroten.
Sorry for my ranting. I just wanted to share my germinating experiences in case it helps out.
In any case, I just looked up root riot. That seems pretty solid as a medium for germinating or post germination. I dont know how the PH is on those, but I know that certain organic cubes tend to have a higher PH than what you probably want. I am not saying these do, though. I would put a seed in there about the depth of a seed (3mm?) and have it just covered over with something. On my rapid rooters I tore a small piece from the side and kind of layed it in the hole on the seed. I wouldnt put seeds too deep or they will take forever coming up if they do at all.