There is a trim piece that snaps over the screws that hold the larger sill plate down. Same system holds all the sill plates in your DII down. Look closely and you can see the difference in the plastic finish. Use a sharp knife to pop out the trim piece then remove screws. Slide the sill plate to one side and bow it in the middle to clear the quarter panel trim, and then lift the sill out. Install in reverse.
I think the thickness of the carpet and the padding will make the sill plate fit poorly over the cargo-liner, especially at the ends near the quarter panel trim. You could remove the carpet and replace the whole thing with rubber matting, might work better. The carpet is a different piece from the passenger area carpet/pad so you could remove just the one.
Wheeling in Florida has made me a master at disassembling my interior. Now however, I find if difficult to spell well, and I have a strange urge to learn the banjo!