I can only tell you what I've done on two TR6 restorations. I wanted the fuzzy portion of the door seal (the part that clips to the seam) all the way up and beneath the windshield capping, meaning I didn't want it to dead end at the capping, but rather run right up, inside of it, and butt up against it out of sight. To do this, however, I made about a 1/4" slice with an exacto knife of the rubber hollow tubing where it is attached to the fuzzy portion, so the fuzzy portion could run up inside the capping strip, and the hollow tubing portion ran up outside the capping strip, and continued anouther 1/4" to be flush with the top of the capping strip. Get it? The capping strip is in the 1/4" slice, the fuzzy portion runs inside the capping strip, and the hollow rubber portion runs outside the capping strip. They sandwich the capping strip. This way, when you put the top up it seals nicely with the rubber hollow tubing.
Hope you can understand this. Hard to describe.
Jeff