When you first turn on the game, you have a controller select. Just keep tapping the control stick or top button on the Pokéball Plus until it highlights the Pokéball Plus. The top button is like the B Button or Start Button, as the control stick button is like the A Button. Shaking it is like the Y Button or X Button.
If it’s dead, plug it into your Switch and do not touch it while it’s charging. You’ll have to wait three hours after plugging it in before you can unplug it.