The light schedule is pretty easy. 18 hours on, 6 hours off whenever in the 24hour cycle you feel like doing it. Personally I like to leave my lights off during the day so my 6 hours of lights out is done during the day, but then again I have pretty excellent light control in my grow room. I also need the heat from the lap at night to keep the plants warm. You may not, so therefore you may need to incorporate lights out during the night if you cant ensure your plants total darkness any other way.

At any rate, during seedling stage I use 24 hour light until they are about 1 to 2 weeks old or they appear big enough to fit into my normal system like you were mentioning.

I do not sprout my seeds in that system as it is too harsh and not meant for that. For seed sprouting and stem cloning I use a rooting tray with a simple 100 watt cfl light 24 hours a day. I water the rooting tray every other day and I have a heating mat set to medium to keep them warm. This was actually a very large issue for my when I was learning this process too. It is not as simple as sticking a seed into a net cup. With the system you described you will need to grow your plants up a bit before putting them into the net cups and into the system. Your best bet for that is to look into something called Rapid Rooter. They sell them at just about all the hydroponic stores and some garden centers but frankly I was unable to locate one until I went to my hydro shop. Just google hydroponics in google maps and you will find tons of hydro stores in your area. When your talking about what your growing just refer to them as your "plants" and that you are growing tomatoes and peppers as that is the code for marijuana. Do not mention anything other then that in their store or they will toss you out on your arse. With that tray I can sprout seeds or clone from existing plants very easily and then I transplant them to the netpots with neoprene tops and possibly a little hydroton to keep them steady. I plop the entire rooting cup into the netcup as it would be impossible to separate it from the roots.

After about a week or they have at least 4 sets of leaves on them then I move them into my normal system where they will stay for here until harvest. 18 hours light, 6 hours dark and you do that for the entire veg cycle. When you are ready to flower, simply change the light schedule so that you are giving them 12 hours on, 12 hours off. That's what triggers the flowering in the first place is the change in the lights. Once you change the lights, to the new schedule the plants will respond and begin to produce flowers.