The folder templates will be used to install supported templates downloaded from the yeswiki repository.
Templates are used for all kinds of views, but more often for bazar database views.
They are organised by subfolders in the name of the extension (templates/bazar/ for bazar. templates/contact for contact, etc,..)
Those are automatically installed by the action {{update}} in the administration menu.
For your custom templates, please use custom/templates/ (otherwise there is a risk for loosing custom changes while updating your wiki). You can copy an existing templates there to modify them (priority to custom/templates/ folder when two identicals names for templates are used).