how is the apple pencil stored?

If you are referring to the iPad Pro, No.

You will need to find and purchase either or both a separate case and custom Apple Pencil holder or look for iPad Pro cases that have built-in holders for the Apple Pencil

OR

There are sleeves that you can purchase that slide over the Apple Pencil that have a thin magnet built in to the sleeve so you can securely attach the Apple Pencil to the part of Apple smart cover that has the built in magnets that turn the iPad Pro’s screen on/off.

Good Luck to You!

My AVAPO cover has a holder for the pencil on the bottom.