Again, a model gets whatever saves it is allowed to take, the hit just kills the model regardless of how many wounds it has if the fail is saved.
So, if the model gets a cover save, it gets a cover save. If the model gets an armour save, it gets an armour save. If the model gets an invulnerable save, it gets an invulnerable save. If it gets more than one of the above, it chooses which it takes - as normal.
Then, if the model fails whatever save it took, it then dies (barring other special rules, such as eternal warrior), regarless of how many wounds it has left.
Inquisitor Moderatis Ruminahui