Yes, you can!
To add an internal note to a chat, click on the "Message" toggle above the typing box on your chat window. Select "Note" and you will see the box turn yellow.
You can now send a note that will be visible to others working at your clinic, but not the patient. This is easily identified by viewing the messages with a yellow background (internal note) versus blue background when sent / white background when typing (chat visible to patient).

