The holes are filled by epoxy when you wet out the glass. No need to do anything special. Please refer to the thread "western red cedar holes" from a week ago for further discussion.

Thanks Joel that's what I thought. 
I just began wondering when I noticed that some filling had been done in the photos in the manual.

 Hi,

I've now got all the glass on which of course filled the holes there but the timber where there is no glass is not the same. After two coats of epoxy on the interior bare timber and so far one on the exterior quite a few holes remain unfilled. I guess I'm going to have to really force the epoxy into the holes with the final coat before painting with polyurethane or do you think or will they all eventually fill without extra effort?