e107_core/templates/) should be copied into
Some examples to illustrate this:
1) The comment template is a core template, as it is located in e107_core/templates/. To override this template, copy the file to e107_themes/your_theme_folder/templates/.
2) The news template is located in e107_plugins/news/. To override this template, copy the file over to e107_themes/your_theme_folder/templates/news/.
3) The same for, for example, the chatbox menu template. The chatbox_menu template is located in e107_plugins/chatbox_menu. Copy the template over to e107_themes/your_theme_folder/templates/chatbox_menu/
Important: For overriding plugin templates, the folder name within your_theme_folder/templates/ directory must match the exact plugin folder name.