The two timelines relate as follows:
If you set a time keyframe it will be linked to the time the yellow cursor is at in the replay timeline (the upper one). This will tell the mod, that, when playing the path, at the time where the time keyframe is in the keyframe timeline (the lower one) it should be the time in the replay timeline that was set when the time keyframe was created (where the yellow cursor was on the replay timeline when creating the keyframe). That means if you set a time keyframe on the keyframe timeline at 0:30 and the cursor on the replay timeline was at 0:40, the scene from the replay at 0:40 will be displayed after 0:30 in from the path.
I hope this clears things up.