I think half of us pour or spray on the top the others soak up from the bottom. Just don't the beat the young plant up :-)

I spray from top with a mist nozzle since I dont have a bottom wetting tray... For early on days if the nozzle is not set to mist, they may fall flat, so you need to be careful till they grow strong... I mist thrice a day rather than drenching them.... One month on, after they grow couple of leaves i add a mild liq fert.

Water from above. Make sure it is slow and fine stream of water. Strong flow of water will disrupt and lift seedlings out of substrate.

Rick