The USB-C port in the case is for charging your iPad, so it leaves the iPad USB-C port free for other stuff like a hub so you can attach a SD card, external hard drive.
So it's a pass through charger for the Ipad rather than a charger for the keyboard. You never have to use it if you don't want to, it's just there for convince and to make the Ipad/magic keyboard more like a laptop with the multiple ports.
I haven't seen the pamphlet so I am not sure on the wording or what it tells you to do. If you go to YouTube there is a number of videos and reviews about it and they all explain how the port/charging works.
Hope that clears it up