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A Root Riot is just like a Rapid Rooter, but made by another company (I don't like GH). Yes, I pH my water and thoroughly moisten the root riot. I turn them upside down so that the wider end is the base; I learned the first time, that the tinier end won't stand up on its own (see picture).
My germination tray lid has slots on the top which I keep open so that there is air circulating, but the moisture doesn't dry up real fast (I don't want to be in there once an hour moistening the root riots, but I do check them 3-4 times a day). I keep the germination pad around 83 degrees. I just stick the seed in; I don't even pre-soak it.
Out of the six seeds in the picture, 5 germinated very quickly, and one got its tap root broken; R.I.P. Like I said above, as soon as I see them emerge, I put them under light so that they don't turn yellow or stretch seeking light. This is the crucial time to keep an eye on them, keep them moist, and wait for roots to start emerging from the root riot. The moment I see roots coming out (which you DON'T want exposed to any light), I put the root riot in the net pot with hydroton, and put water in my reservoir (I'm a hydro grower). I keep the water high, but not high enough to moisten the bottom of the net pot; I don't want to make lazy roots, I want them to grow down seeking water. I keep watering by hand. As soon as I see roots descending into the reservoir, I add a very weak nutrient solution, turn on the drip emitters, and stop hand watering.
On my first grow last summer, I can't tell you how many expensive seeds I killed, but it was quite a few. Then I started to get the hang of it.
What medium are you growing in: soil? hydro?