You should use the nails (not the copper deck nails).  I used 1" #18 brass brads spaced 6" apart.  They blend in well with the wood colour...you really have to look hard to see them they are so tiny but the have a lot of holding power.  I also epoxied the rails.  Some will advise against this to allow for future replacement if they get banged up but I'm pretty careful. I also extended the 4 oz. deck glass over the rails for added protection.  I think others have used just epoxy (using tape to hold the rails in place).  This seems like a lot of trouble....you really don't notice the little brads.

Chris 

Glue by itself will work fine, too, if you can figure out a clamping method. Nails might be easier.

Laszlo

Thanks for the help- and especially the pic- that is a beautiful looking boat.

Thanks...you can see the whole build at: http://www.flickr.com/photos/algonquinpaddler/sets/72157594510381189/