There is a battery widget you can use to see how much remaining battery Apple Pencil has.
Open Notification Centre by swiping down from the upper edge of the screen. Scroll down to the bottom of the left column and tap the Edit button.
Scroll down to the Batteries widget and tap the green plus if it isn't already under the left or right column headings. You can drag it to the column and position you like by tapping and swiping on the double lines to the right of the widget.
Tap Done to close the Widget editor.
Now you will see the battery widget in the position you choose. Place the Apple Pencil in the Lightning port of the iPad to see the battery level if it isn't showing.