Yes, fill the gaps to the maximun extent that you can.  If you don't fill them, they may fill with straight epoxy when you wet out the glass, but that is heavy.  If they do not fill with epoxy, the air in the gap may cause the glass to bubble up as the epoxy cures and warms.  If you have any large gaps, use a sharp knife to cut a sliver of wood to fit.  For the outside of the boat that will be seen, use epoxy thickened with a mixture of wood flour and cab-o-cil (silica).  Play with the mixture until you get a color that is close to the avareage color of your wood.  Even if it is off by a couple of shades, you will barely see it once the boat is glassed.  For the inside that will not be seen, you can use epoxy thickened with microballoons.  This mixture is lighter and much easier to sand.  Picture is the underside of my Mystery deck after the seams have been filled but before sanding.

   Thank you, Mark! Appreciate your helpful tips.

Hi Patrick,

another approach that i use for hairline gaps on the outside (less than 1 mm wide), is to put a thin bead of the wood glue on the gap (i use a small glue bottle of wood glue with a sharp end just for this purpose).   then before it dries, with 80 grit paper, i gently sand slight across it moving from the lighter strip to the darker strip.  the sawdust will mix into the glue forming a putty that matches the wood and the gap will disappear.  

to keep things clean, I also typically use inexpensive blue painters tape along each side of these gaps to keep the glue from getting all over the place.  (so tape either side of the gap with blue tape, force wood glue into the gap, wait a couple minutes, remove tape and gently sand with 80 grit sand paper pretty much following the grain).

the advantage of this method, particularly on the outside,  is you get a great color match--  the crack literally disappears and is undetectable and it’s easy to do a bit at a time without the hassle of epoxy and pot life.  I find that before I glass the outside of the hull, I will typically spend a couple nights just to get all these little gaps gone…..and it would be a huge hassle to do that tedious work if you were also working around the pot life of epoxy.

On the inside gaps, I typically use epoxy with micro balloons (similar to what mark described) but I typically try to make mine peanut butter consistency…., and use a plastic putty knife to push it into the crack.   again, I will typically blue tape to keep things clean and have less sanding.

h

   For visible areas I am a fan of gluing in slivers of matching wood and planing smooth.  I never found any filler that matched as well. On  areas just too small for a wood sliver I saved sawdust from the matching wood colours to mix with epoxy, but it wasn't as good.

   h and Richard, Thank you both for the additional techniques. I love how there are several ways to skin a cat so to speak when it comes to these issues. Great info as always. Cheers from Colorado!