In the lower left corner of the screen (upper left on an iPad) you'll see a button for messages. There are several types of messages that can be sent or received in the system.
System messages are generated automatically, and contain information about practice audits or changes to your schedule that were initiated online. The practice audits are conducted each Monday, and will list patients who have suddenly stopped scheduling appointments, patients whose precertifications will expire soon, and days when you have forgotten to chart or lock records. If a patient is sent an automatic birthday greeting, you'll get a notification of this, as well.
Patient messages are "secure emails" sent by patients (or potential patients) from your online schedule page. You can reply to these messages through an encrypted, HIPAA-complaint channel by clicking on a "reply" button. You can also initiate a secure message to a patient by displaying the patient's information, and clicking the "Send Email" button. Important notes: this button won't appear unless the patient has an email address on file. The message will not be secure unless the patient has established a password for himself (you'll be warned in red if this is the case).
Coworker messages can be sent to others in your work group. This is a good alternative to email, because these messages are encrypted (and thus under HIPAA can contain Protected Health Information about patients). Click on the "New Message" button at the bottom of the list of incoming messages in order to initiate a coworker message. You can click one or more checkboxes if you want to send the message to multiple recipients. You can also forward messages on to another person.