I was partially mistaken. The seal in the picture is for both the leading edge and the bottom of the quarter window (#11), the other one (#12) is for the rear, vertical seal. The best I can figure is that the larger groove seals against the thick door and the bottom channel and door and the smaller groove is for the glass. Keep in mind that from the outside, all three of the pieces look the same (i.e. slim rather than the thicker appearance the leading and bottom pieces have looking from the inside. For the #12 piece, I believe the wider groove seals against the aluminum channel and the narrower groove against the glass.
The only pictures I have are from the exploded diagram I referenced and the r.d. enterprises picture. I looked at my car and it's hard to get much more of an idea about it. I think the key is that all three pieces look the same from the outside. My guess is that once you arrange it so that looks like what will happen, it will become clearer.
Let me know if that helps.