When your roots are long enough that at least one or two inches gets covered when you flood the system, then you should put them into your system. Otherwise you leave them in your tray where you can make sure the roots are going to get moisture.

If you've got a 6" net pot, you'll usually start seeing roots coming out 4-7 days after putting the plants in. As long as the plant looks like it is not dying, even if it looks kinda dormant, it will be OK. During the first week or sometimes even two, after the plants are in the system, it usually looks like they are not doing anything. Then one day you'll look in on them and say "woah, what happened? I don't remember you guys being this big!" I would just keep the light back a ways until they look like they've started to grow good. Then keep it as close as possible, but move it closer gradually over a week or two. Good luck.