The easiest way to send a secure message to a patient is to hit the blue Secure Message icon on their profile photo in the patient dashboard. If the Secure Message icon is not blue, the patient will not be able to access the message. More on granting and trouble-shooting patient access to the portal is here.
Click on the blue Secure Message icon to launch the Secure Message window. There, add a title to the Title: field. Write your message to the patient in the "Message to Patient:" text area just below there.
You can choose to notify the patient via email that they have a secure message waiting for them in the Patient Portal by checking the Notify Patient box below the main message window. This box is checked by default, but you can uncheck it if the patient does not need to be notified that a secure message is waiting for them.
At the bottom of the Secure Message pop up, a gray link and icon called "...Show past correspondence with this patient" will let you view past correspondence with the patient via Secure Message.
It is possible to send Secure Messages from other areas of the EMR, as well. Anywhere you see a blue Secure Message icon, especially in the Patient Portal queue, you will be able to send a message to the patient by clicking on the icon.