Merlin is a document based application where data is saved in individual files. Like most other document-based applications, Merlin files can be based on pre-defined templates or saved as templates.
It is also possible to save any project file as a template. User created templates are listed among the bundled templates
If you want to edit your template, open it using "File - Open" menu entry and navigate to the location of the template. Default location is "~/Library/Application Support/Merlin/Project Templates"