Wait til the have a couple of sets of true leaves (those long thin ones you see now are called cotyledons). It's usually best to handle them by the leaves, as a lot of stems are surprisingly fragile. Just kind of ease 'em out of the egg carton with the help of a popsicle stick or whatever, rinse off the roots so that they're clean, and pop 'em in your bed.
Might help to not have the lights on for a while if you have HID lighting. Misting plants a couple of time a day after you transplant them (again HID lights off) helps a bit too. Since they go through a little bit of transplant shock. I usually take this opportunity to mist with some Kelpak/MaxiCrop/Seasol type product (growth regulating hormones extracted from kelp along with trace elements). I've done some side by sides with Kelpak and no Kelpak in the misting bottles, and it does seem to help them recover and take off quicker.
My water is constant flow about 2 inches below the surface(Tried the bell siphon...still working on it.) How far down in the gravel should I plant sprouts? And does anyone sell lettuce spouts in bulk if I ever wanted to make a larger operation?