Are the paid PE tickets one way or return? Each passenger will only be able to board with one boarding pass, so if one boards with the J pass then they will be a no show on the PE ticket and have the remaining sectors on that ticket cancelled. If they board with the PE pass the J seat will be a no show and the manifest will show no passenger sitting there. You won't be able to scan the two passes as you can't have the same passenger occupying two seats.