Does anyone know how to organize this game while playing?

I gave up too because my eyes got tired lol

For me, I sell level 1 items when I don't need them. I pick a specific item (like a Flower of Life), keep merging them, and if I succeed in reaching a new level, I sell all but the highest level achieved. Lower level items are just merged in groups of three.

I keep the things I don't need right now in orb form and pop them when I need them. And I decide on a few things to merge slowly, merging only those, and adjust other types to take up as little space as possible. But honestly, none of that matters. If you just merge the eggs you get from events when you have three, and sell the ones that are left with one awkwardly, you'll get quite a bit of space... lol