Yes that is correct. You send a constructor a resource it builds a resource base. You try to build a base somewhere else you'll get asked military, cultural or economy. It is important to build resource bases to give you an advantage, also to deny your enemies use of it. Even if its not in your play book. Like for example influence resource when you are conquesting your way militarily. As for research/morale/economy those will help any strategy your going for. Combat resource = must have / must deny enemy.

For the upgrade, I just have to choose mining upgrade if I want a better bonus output?

Yes, works for all kinds of resources.