How to repair deep scratches on wood duck?

I finished my wood duck hybrid this spring and due to the assistance of this forum it actually turned out ok. I bought a kayak rack that is on the wall of my garage and managed to put several gouges in the hull down to the fiberglass. The fiberglass is visible but I cannot feel the texture. Here is where it gets ugly.  I had as small amount of varnish left so I thought I should just touch it up with varnish and it would make the gouges dissappear.  Bad idea. I then read on pygmie boats site that I should have sanded it down to the (now varanished deep scratches) and apply epoxy then varnish.. OOPS. I tried just some hand sanding , applied epoxy, and the fiberglass did not dissappear. Maybe the varnish prevents that?? Sand deeper? 

So my varnish has hardened, I cannot be certain of where the epoxy went since the scratches are not  just a simple staight line and I realize I should just revarnish the hull.  I ordered 1 pint of varnish. I will do an orbital sand of the hull to clean it up but.... how do I get the gouges and fiberglass weave to dissappear if possible? I will sand down on these areas and apply thin layer of epoxy then varnish or am I missing something. Keeping in mind the scratches are not visible when the kayak is in the water. thanks

Sand down to bare wood on the damaged areas to remove the damaged glass and apply a glass patch.

If the damaged areas are small enough, you can just paint them with epoxy after sanding and not bother with the patch.

Laszlo