The simplest approach is to use a layout based on one of the primary tables, Pilots, for example and place a portal to the join table, not planes on the layout. To link a pilot to a plane, you add a record in the table and select the ID of the plane in the drop down list in the portal row. This requires that "allow creation of records via this relationship" be enabled for the Pilot to Join table relationship.
Here is a many to many demo file you can look at and work with. Feel free to ask questions about what you find in this file if you encounter something that you do not understand.