Hi Captain Canuck,
In order to get help on a specific mission you should ask on the SSE > Missions board. Please read the bold blue topics on that board for guidance in finding, or asking for, information on specific missions.
In general, when you cannot zoom out far enough on the chart to find a waypoint marker, you can be guided by the CTW below the conning circle, and if you activate the middle button, the small open circle on the conning ring. Although the CTW is the direct bearing to the waypoint, it should allow you to proceed until the marker is visible on the chart.
Use of the autopilot in missions should be restricted to covering long distances in fairly open areas, and only when you know where the next mission waypoint is. Otherwise, the autopilot might conflict with the operation of the state machine that controls the mission.
Specifically you should never set an autopilot waypoint over, or even close to, a mission waypoint. The trigger to advance the mission state may take place hundreds of meters in advance of the center of the waypoint.
Also, there may be triggers that are not visible on the chart, such as those that affect the weather or sea state. You could miss them or trigger them in the wrong sequence.
Regards,
Marty