My dragons eat mostly Diamondates and Rushrooms, with a few Upgrapes when there's time to grow them. I have my habitats mostly sorted by color, and the special ones and/or habitats that I just have one of each go in the upper island. In the mining expansions I put some spare habitats with repeated dragons that I'm keeping to trade. Also, all my farms are together in one of the smaller islands, as are the other buildings (breeding den, nests. etc.).