Alan: Please review this link http://www.westsail.org/westsailFAQ?mode=MessageList&eid=491881 for how several have handled the caprail sealing.
In short, you don't want to glue down the caprails as removing them later would probably destroy the caprail material. Rather most will clean up the fiberglass joint area and fill and level off the area with your choice of sealer - in my case Life Caulk (sp?) let it harden / cure and then install the caprails. See the above for details.
Jay