Empty schema and how to override

After creating a new template (using Handlebars starter for example) the options file is empty when using Edit Template Files from the edit menu. Any changes made to the options.json file are over-written when the form builder is used (the form builder is on by default on all templates we create). Is there a way of adding to the options (e.g. "configset":"standard" for the ckeditor) when using the form builder or can the form builder option be de-activated?