Hi Stan,
Lou is quite right about "playing" with the Trainer being the best way to learn. However a few "functionality pointers".
1. To enter an ID Code (airport, VOR, waypoint etc.) you need a flashing cursor, which is activated by depressing the small right-hand knob. In the sim this is normally done by depressing your mouse scroll wheel when the cursor is over the small knob
2. To select the 1st, 2nd, 3rd etc. characters of the code, use the large RH knob
3. To select the letter or number for each of the 1st, 2nd, 3rd etc. characters, use the small RH knob
4. When the correct code has been fully entered, enter it with the ENT button
5. For a Direct To waypoint the flightplan is automatically activated when you use the ENT button (one of the prompts is "Activate?")
6. For multi-step flightplans you may have to use the MENU button and select the Activate Leg ? option.
Edit:
As for flying the route in the Trainer, there should be some controls in the Trainer window below the GNS itself (see image.) Just dial up an appropriate speed and altitude (entirely academic in the Trainer) and you can see how the GNS behaves. By default the "autozoom" option should be enabled, and as you approach a waypoint the scale should reduce a number of times until the waypoint is reached, when the scale will zoom out again to encompass the next waypoint.
Alastair