In order to use custom fields in your own email templates, you should start adding/editing the template using the instruction here.
You can put custom fields to the template in 2 ways:
1. Using name
$issue.getCustomFieldValue($customFieldManager.getCustomFieldObjectByName('Name_Of_Custom_Field')).toString()
where ‘Name_Of_Custom_Field’ should be replaced with you custom field’s name
2. Using ID:
$issue.getCustomFieldValue($customFieldManager.getCustomFieldObject(Custom_Field_Id)).toString()
where Custom_Field_Id should be replaced with your custom field’s ID