couple ebb questions

so i have 4x4 40 gal ebb and flow system and i want to use just that one tray to flower i have 36 spots and plan to harvest 9 plants every 2 weeks can i have the same water settings in the same tray? because i will have the clones and the other bigger plants in the same tray. can i do that or do i have to change it into a drip style system and control water supply to each different sized plant?

I use the same strength nutes on all my plants except seedlings and new clones. I always flood the system every three hours regardless of size or otherwise.