Can I send different files to different recipients in the same email? If so, how do I do this?

 Yes. In the second step (Compose) of creating a Certified Email, you can choose to attach the same file(s) for all your recipients, by dragging them into the For All tab of the Attachments (Optional) section.  

To send different files to different recipients, you must do so via the By Recipient tab of the Attachments (Optional) section, by dragging the files into each recipient's respective box.

Files sent to a specific recipient will only be visible to that recipient.