Updated comments after Ricardo's suggestions.

README.md

@@ -13,8 +13,11 @@ Examples and documentation will be added/improved over time
 
 ## Templates
 
-Coordgen uses templates for some macrocycle systems. The default templates are in `templates.mae`. If you need additional
-local templates, use `CoordgenTemplates::setTemplateDir()`, and put them in a file called `user_templates.mae`.
+Coordgen uses templates for some macrocycle systems. The source for the templates is `templates.mae`. If
+you're an end user of coordgen, you can add local templates in a file called
+`user_templates.mae` in a directory specified by `CoordgenTemplates::setTemplateDir()`. If you want to
+update the templates, add new templates to `templates.mae` and run `mol_generator.py` to generate the
+source files.
 
 ## Usage example