The bottom cups are just basically the catchers, filled with a little hydroton for elevation. Also placed a lil hydroton at the base of the main cups for better drainage. Got this idea from hempy cocos.
Whoa..nice looking. I've been using your seedling photos for comparison, mine are 8 days now and don't look near as nice yours did. My leaves aren't very big. Got a second set coming into view though. Headed to grow shop, they have a tea brewing all the time, no nitrogen. thought I would start a diluted feeding. Using the same mix as you too.