A good tip is to preserve all your food when you’re doing Atlantis. It takes food to clear out your recruits and put them into your TC.
During Atlantis I avoid building, making crafts, ascending heroes, placing emblems, adding to TC 20.
I put everyone into TC 11 and only feed heroes when my roster is full.
After Atlantis I deal with the 1000+ days I have in TC 11 and build my battle items, ascend my heroes, etc.