You will not have to change the whole sill specially if the drama was not visible last year.When the rot finally shows you usually only have to deal with a 200mm section.
The easiest repair which involves a lot less work is to cut out infected area and mig weld a new piece of metal in place.Welds can then be ground down,filled,stonechipped & painted.
A faster,less pretty way is to overplate the infected area & slap underseal over it.Get it through the MOT but looks horrible & if you decide to fill over the joints at a later stage you'll need to spreading filler further up the rear quarter to lose the joint.Get the plate migged in for an easier repair!
If you're unlucky enough to need a complete sill you'll have some paint repairs to be getting on with on the rear quarters & door shuts.Oversills must also be seam welded for the MOT unless you hide the spot welds well from the hawk eyed MOT tester.
The water gets in the sill from the rear inner arch,there is a hole about 100mm up from sill bottom where the inner arch goes at right angle.Sorry hard to explain but it's definately there!I'll try posting a pic if you want to fill it in....