Hi Chuck,
Not sure how the seal is held in place but the general principle with seals is the open end faces outwards. This ensures that any ingress from wind or water etc forces the seal open which increases the seal efficiency. I have my hardtop on the car at the moment but have checked my soft top which is wintering on the bed in the spare room ( don’t tell the wife though, she things it’s going back in the garage very soon). This has the open “V” of the seal facing out. I also notice that this seal fits into a channel and does not require any glue. Another thing to check is that you still have the small top hat seal that fits in the rear centre of the hard top to cover the soft top latch hole. If this is missing you will get lots of water in the soft top tray.
Good luck
David Brough
1969 280SL