I agree with glh421 about creating override folders all at once, but some here think you should only create a override folder when (and where) you need it. Either way works. Everyone agrees you shouldn't move files into those folders until you modify them.

The manufacturers.php file you were looking for is in includes/modules/sideboxes (and it's overridable) , but you shouldn't have to change it to get the sidebox to show. Are you sure you enabled it in Layout Boxes Controller on either the left or right?