Hi,
Acrobat Reader for iPhone and iPad supports Apple Pencil only in the "Freehand Drawing" mode.
- Open a PDF document.
- Long-press on an empty area (i.e. no text underneath) of a page to display the context menu.

- Tap Freehand in the context menu.
- Start drawing with Apple Pencil.
- Tap the Save button in the upper-right corner to save the drawing.
The default color of drawing is red. But you can change properties (Color, Thickness, and Opacity) once you add drawing to a page.
To change Thickness/Color/Opacity
- Tap an existing drawing.
- Tap Thickness.../Color.../Opacity...

- Select your desired Color/Thickness/Opacity property from the palette that pops up.
Hope this helps.
Please let us know if you have additional questions.