Each empire in the game can store an unlimited number of resources at the empire level. The exception to this rule is that an empire may only store research points equal to the total capacity of all research buildings within an empire.

Resources are generated and stored by buildings at the nation level. One way to get resources stored at the empire level is to complete quests because the rewards of all quests are stored at the empire level.

To use the resources that are stored by an empire, you will need to navigate to the nation view page within your empire and select Empire Resources from the Nation Action Menu.

Doing so will show a popup dialog that will allow you to transfer resources from the empire to that nation. You may not manually transfer resources from a nation to the empire.

From the pop-up you can see how many of each resource is stored at the empire level and that of the current nation level. You can choose how many resources to transfer from the empire to the nation and press the green button to move resources from the empire to the nation.