To add a database to the workspace click on the "Add Database" icon on the toolbar or click on the "Add" item under the Database menu.
On the Add Database dialog window choose the server where the database you want to add resides. You can click on the "Refresh" button to discover the SQL Server instances running on your network. If the application is not able to discover the SQL Server instance you are looking for either because it is not exposing itself, or it is not running on your local area network, or it is not listening on the default port then you can type in ServerName (or IP address)\Instance Name on the drop down box. If the SQL Server is not listening on the default port you can specify a custom port on the following format: [ServerName or IP Address]\[Instance Name],PortNumber
Once you have chosen the server and the authentication method (including login name and password if you chose SQL Server Authentication) you can click on the "Refresh" button next to the Databases box and the application will connect to the server using the information you provided and populate the Databases box with the list of all user databases in that server. You can select one or more databases to add to the workspace - use the Shift or Ctrl key to select multiple databases.