Upgrading Buildings is integral to keeping your City standing, night after night. To do this, you will need to use some of the gathered resources, such as wood, stone and metal. Sometimes, an upgrade will require more of a resource type than you can hold in your stores.
You will need to upgrade the relevant storehouse to increase its capacity so you can fill it to brim with building goodies.
It's important to balance missions with daily City upkeep otherwise you may find yourself out of defenses and out of time.