Before building your form, we recommend reviewing Best Practices for Building Custom Forms designed to help you make the most of the clinical notes feature.
When a template is made persistent in the form builder, it only applies to the fields created in that template. The notepad section exists outside of the form and is not included in the persistent setting.
The yellow notepad is an extra place to put unplanned notes within your clinical note.
If you would like a persistent notes field for your template, add a Short Text Field to the desired form and make that form persistent.