Apple Pencil with Pages

Normally, you simply have to plug the Apple Pencil in your iPad and wait a couple seconds until it is detected...

As of Pages version 4.0 the Apple Pencil is now supported. This Apple Support for the iOS version of Pages explains how to use the Apple Pencil to draw, mark up and otherwise manipulate a Pages document.

From Apple:

Use Apple Pencil: Tap and hold Apple Pencil anywhere on the page.
Draw anywhere on the page or in the drawing area; you can do any of the following at any time:

• Switch drawing tools: Tap any of the tools at the bottom of the screen.

• Change colors: Tap the current color at the bottom of the screen, then tap a new one. Swipe left to fine-tune your color.

• Resize the drawing area: Drag any of its handles.

• Adjust the color’s opacity: If you’re using the pen, pencil, crayon, or paint tool, tap it then drag the slider.

• Adjust the stroke size (line thickness): If you’re using the pen, pencil, crayon, or eraser, tap it then tap a stroke size.
  

As of the time I am writing this, the pencil doesn't work with Pages.app except as a pointer. It can do whatever you can do by pointing/touch, but you can't draw or annotate.

I researched this on Apple Support and elsewhere, as I was hoping I could draw within the application.

One possible workaround is to export a pdf or image of the page and annotate in another application.