I placed the stones in the bag I found that holds stones. Now I can't get the stones back out of the bag so I can throw them, Does anyone know how to get the stone back out of the bag?

Equip the bag as you would do with a weapon (on either the left or right hand). With the bag equipped, you'll be able to throw stones by only clicking the correct weapon button.

Thanks. It all makes sense now!

And that answered my question as well. Thanks.