First you need to be using version 3.8 beta 3 or later. Previous versions do not support the SSL option.
Next you need to enable the SSL option in your server configuration. Select the Manager tab and edit your server settings. On the General Settings tab under the Server Nickname field there is a checkbox "Encrypted Server Connection (SSL)". Check this box and there will be a dialog asking if you wish to change the port to the standard NNTPS SSL port of 563. If you manually change the port next to the server address then you will not see this dialog. Click Yes then Click OK to close the Server Setup window.
Now when you connect, it will be a secure SSL connection for that server. If you have multiple server configurations, you will need to make this change in each configuration that support SSL.