How do I modify the Questionnaire Emails that are sent to my clients?

You can customize the default questionnaire email at the following link, https://app.shootq.com/controlpanels/questionnaires#autoemails. Remember that this is the questionnaire email template that ShootQ will use when all questionnaires are sent, so it's best that this email is not specific.

There is only one questionnaire email template, so you cannot have a different template for different questionnaires. Your only option would be to create an email template you would like to be sent with a specific questionnaire, then select that template when you manually send your questionnaire. This will not work when sending a questionnaire is a part of a workflow.  For workflows, the default questionnaire email will be sent.