I haven't done this, but will be in the near future (when I get my rear gate parts! Got barn doors now)
The seam will go at the bottom. (gravity will pull water through if you put the seam at the top)
You know, thinking about it, I wonder if you could cut it to fit, and then glue the ends together with the glue from a bike inner tube repair kit. It might help to keep the seam from opening up as the weather stripping shrinks over the years. Plus it'd seal it so water won't creep in.
Again, I haven't done it, but when I do, I think this is the way I'll go.
-Brad
