Upgrading buildings gets rather tedious after a while, may want to try and streamline it or make it so you can upgrade all buildings of a type in one go.
You can press D to select all buildings of the same type as the one you hovered your mouse on. Or use the S hotkey (details on how to use is in the instructions, outside game)
 "Shop Empire Underground"){kind=icon}
 "Helixteus II"){kind=icon}
 "Idle Raiders"){kind=icon}
I know, I already try to watch more mickey mouse club on TV with my son, but it's not help :p