I have a Skoda Fabia 1.9tdi ATD engine, will the later 6 speed gearbox fit my car, as the gearbox is noisy and needs replacing

You don't need a six speed box, that's the beauty of the ATD, a nice wide torque curve.

In any event the old six speeder is fragile and elderly now as well as very expensive and sixth gear will be too tall for a PD100.

Replace like with like to avoid unforeseen problems.

6 speeder plus all the ancillaries to make the wheels go round is generally more expensive and heavier.