Create a new trail here or select a trail where you want to add wayoints to (use the maginifying button for that trail).
Don't forget to use the full-screen button! This will also keeps your phone awake.
Long-press 'Insert Waypoint' to add a waypoint to your trail at your current position.
You can delete a waypoint by using a long-press on that waypoint and long-press on the garbage bin icon.
You can move a waypoint by using a long-press on that waypoint and long-press on the pencil icon. Now you can drag that waypoint to a new location.
You can add a waypoint manually at another location then your current position, by a long-press on the map. Make sure to zoom in first.