How do I customize the e-mails for the referral notification and invite system email templates?
You can customize the appearance of the notification e-mail by using Magento's transactional e-mail system. You can create a new transactional e-mail from the Magento back-end System menu section. You can duplicate the one that is set as the default for MageRewards's referral system notification messages. Once you've done this, you can go into the referral system configuration and set that new e-mail template for your store view.
You want to copy from the "Confirmation" e-mail template. I'm sorry the naming is a bit ambiguous (we've changed this in newer versions). When you're creating your own custom transactional e-mail you may also see two "Confirmation" templates. Select the second one if that's the case (also fixed in later versions).