You do not have to choose "Printing on Both Sides" if you want to print on the pockets. As the folders are printed flat and the pockets folded over, they will be printed on the same side of the sheet as the outside of the folder. Double-sided printing should only be selected if the content is needed on the inside other than on the pockets.
One thing that will need to be kept in mind is that content on the inside of the folder will be covered by anything placed into the pockets. Therefore it is common to see interior printing when there is only one pocket for holding documents so that the other side (and the content) will never be obscured.