Players can use the "Store In Zoo Depot" cursor tool to remove items from the zoo and put them into storage. Currently, clicking on a habitat with this tool will cause the habitat and all animals within that habitat to go into storage. It is not possible to store only one animal of a group, or to put animals into storage without also storing the habitat they're in.
In storage, identical items are consolidated into one stack, with the quantity of items displayed in the upper left hand corner. For animals to "stack" they must be of the same gender and (sub)species. For habitats to stack, they must be the same type and upgrade level.
All items in the zoo depot can either be sold or placed into the zoo. Even if stacked, players can only place one item/animal into the zoo at a time.