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You want the roots to come out of the cups, all the way down the drain and into the res. Those coco cups are fine, personally I don't use them, I just stick the clones into some rockwool cubes, drop them to the bottom of the web pot and fill with hydroton. The roots will go through those cups no problem - I used them once and they worked good, I see no difference without them though.
Keep the water level in the tubes high, like half a centimer over the bottom of the webpot sitting in the water. Soon as the roots are like sticking out 3 inches or so - drop the water level to about 1 and half inches deep, or a centimer or so from the bottom of the webpots - shouldn't have to adjust that for the rest of the grow if you do that.
What size pump do you have? How many GPH is it? You could go ahead and leave the water pump on 24/7, I only turn mine off when I change the res.
Those nutes are probably just fine, I haven't ever tried them so I don't know - I just use foxfarm, it's cheap and easy to get. You need to get a TDS tester or some kind of PPM wand and something to check PH. Some PH up and PH down are handy too.
Just feed them slowly - like 800 PPM at first and ramp it up to maybe 1100 to 1200 PPM. Late in flowering I like to try and push it up as high as I can get away with right before I flush them. I have hit 1900 PPM and had stable PH and plants show no stress, just depends on the strain I guess.
If the PPM goes up, add more water, change res every 7 to 14 days, you should be able to tell when it's ready to be changed by how nasty it starts to look at the bottom.
I'll post some good pics to show you the roots and all what I mean here later on tonight.
If you have good roots showing you could go ahead and go 12/12 anytime, they will keep growing.