I have found the single most important aspect of good growth from the Tower Garden (assuming you are following the basic directions like adding water and nutrient solution) is the health and strength of the seedlings. Joe Daugirdas has been a great resource to me in all technical aspects of growing well with the Tower Garden, and at the bottom is a link to his seedling growing procedure.
The following videos generally follow those guidelines. I hope they serve you!
TG Seedling #1: Prepping the Rockwool
TG Seedling #2: Tray Inserts
TG Seedling #3: Shake Rockwool Dry
TG Seedling #4: Tray Inserts for JP Tray
TG Seedling #5: What Kind of Seeds?
TG Seedling #6: How Many Seeds?
TG Seedling #7: Seed Germination, Feeding, Recording
You can find Joe Daugirdas Seedling Growing Procedure here.