Can you manually add waypoints in the FSX flight planner? 

You can manually add any waypoint that exists in FSX... you cannot add user waypoints.

 

DJ

In the FSX planner just drag the line and a new waypoint appears.

Matt,

 

You can manually add waypoints to a flight plan in the FSX Flight Planner.  For a quick try out, set departure and destination airports, On the "Create" tab, select departure and destination airports, choose either VFR or IFR, and for routing select Direct - GPS and click on Find Route.  The planner switches to the Edit tab, showing a direct red line between departure and destination airports.  Click, hold, and drag anywhere on the red line.  This will create a WP1 waypoint.  Note that you can also edit these custom waypoints by changing their lat/lon, elevation, or even add a description.  

 

Have fun.