The code cyphers card is very simple. On the right side of the screen are a list of cyphers which might be used to encode a message that is sent to the ship. Clicking on the cypher shows the characters which represent the English characters. A print button allows this code cypher to be printed (which requires the printer to be configured beforehand).
The intention is for printed messages to use the special fonts to encode the messages. This is easily done with the Code Cyphers core.
Simply type the message in the top box and choose the code cypher you wish to use. That message will show up as an encoded message which can then be printed from the Core computer to a printer on the bridge of the simulator.