When you manually enter a payment, the system should give you the chance to edit the email to the guest. It defaults to what you configure as the "Send Receipt To Guest" template, but an editor will open so you can tweak it. Most system events are like this, with a customizable template and then availability of the editor to add in personalized things if you need it.
If you need to send a custom email that's not related to a system event or triggered automatically, the best way to do it right now is to click on the email address on the Booking Info tab and send through your own email program.
We are working on a fully customized system that will manage all emails inside OwnerRez vs. requiring you to use both your email (for custom things) and OwnerRez (for automatic system things). I'll keep you posted as we get closer to rolling that out.