The link shows another type of cap for a Yamaha bike, but I think I get what you're talking about. There is a small rubber seal that goes below the tank fill hole. It needs to be aligned with a mark inside the cap since there is a small vent channel that goes through that rubber seal. I left it there and aliggned the cap with it.
Just checking, the part number you're using is TF041? (the A or B on the end is for the color)