I'm sure that you are referring to that door sill plate , the black plastic strip. I have discussed this online and IP with many ppl about this "annoyance" design. This is a design flaw that can eventually cause the door sill underneath to rust if water accumulates, which it will on an S series every time you wash it or it rains. I frequently noticed this on customer's S cars.
That strip is attached by 5 or so brass push clips that press into thin slots on the body to attach it. The water has nowhere to go and is held under this plate and will eventually cause rust. On my SC2, I had to gently pull this strip up every time I washed the car or it rained heavy, dry it and replace it. That's one of my pet peeves with the S series.
AFAIK, there is no drainage there on any S series, only the metal clips and holes. You can do either one or the other, replace the strips with brand new ones and they will seat better. OR - seal the plates on, making sure that all the edges are sealed. I was considering 2 sided tape as this is less intrusive and more sure than glue. You will have to use a tape the width of the plate to properly seal the plate and prevent water from getting underneath. And the tape will be removable, glue is permanent. Replacing the strips is the most costly but will greatly reduce the water retainage, yet you will still have to dry that area every time it gets wet or it wil continus to rust.
BTW - there is a chemical called I think - Great Stuff rust converter liquid. It will convert rust to black primer and kill any rust that htis problem has caused and help aid in preventing future rust. Careful, it is an acid, keep it away from plastic and good paint.
Best of luck though.