All automated Nation costs, such as founding Towns and paying daily taxes, are withdrawn directly from your Nation Coffers. When in a Nation, any ender chest that you open in your own Town borders, or in an NPC Town, will open your Nation Coffers chest.
Gems must be physically withdrawn and deposited at an ender chest. You can access ender chests at the Bankers in Nauru, Telaria, Eastwind, and Port Qi'Shen. All Town Halls will spawn with an ender chest inside, and additional ender chests can be purchased directly from your Town Steward.