David,
See
here for a recent thread on the subject.
The water gets onto the sill plate from drainage holes under the door, and by running down the A & B posts. On the SE there is a very small lip on the plastic door sill, as you've noticed: S2s have a much taller lip. It's to stop the water which runs down the A-pillar seals or B-pillar pouring into the car instead of out under the door. There may also be a couple of inverted V-shape notches cut in your door seal at the bottom to let the water drain out (point 4
here)), or a couple of plastic nipples to break the seal at the bottom and let the water out. In addition, I extended the sill lip by Sikaflexing a bit of rubber beading onto it.
Also see
here for the waterproofing addendum to the Service Notes. Have a read of pp 55-73 to get some ideas. One thing - if your front hood seal is leaking, don't follow the "drain tube" advice on P73, but rather add some extra foam seal to the top of the windscreen (or silicon sealant - use cling film on top while curing to prevent it glueing itself to the hood seal) to prevent water getting in past the header seal in the first place and dripping down at the A-pillar.
John