: Everything was clear before I started to sand it. The surface is
: still rough. I did sand it down to get rid of the high spots so
: that the varnish would lay out more smothly. Was I wrong in
: sanding it to creat a flat surface? I thought that it would be
: ok just as long as I didn't sand through the glass. If I wet it
: out with water and it doesn't dissapear, epoxy won't cover it up
: either? right?

You weren't wrong in sanding. Even if you aren't looking for an 'automotive-grade'/'guitar-grade' smooth finish, you need to knock off the inevitable bits of dust and other 'hairy bits' before varnishing. To get a completely smooth finish, you need to sand until the entire surface is an even dull texture. This can require adding more epoxy 'as you go' to avoid sanding into the glass, i.e. sand down the high spots, add epoxy, wait for full cure, sand smooth.

Those pics look like just dull, sanded high spots to me.

How well is the epoxy sanding? If the epoxy isn't cured 'hard' (this can take days of warm conditions after it is cured 'to the touch') it will sand to a 'rubbery' surface (and clog sandpaper like crazy). That will make the sanded spots look 'white'.

Sanding with dull paper can heat the epoxy and soften it, and result in the same 'white' look with dust mixed with softened epoxy.

Wet sanding (water and a drop of dishwashing detergent, using wet/dry sandpaper) usually works better for me.

Don't be afraid to experiment a bit. With epoxy, you can always sand off extra. Taking cured varnish off a non-smooth surface is more work, but with stripper and a bristle brush it can be done. Uncured varnish will come off with paint thinner and a brush/paper towel.
Put a swipe of varnish on a non-conspicuous spot (sheer line at one end?) and see if the spots go clear.
Mix a shot of epoxy and do the same.

Work on the hull first to get your technique worked out. Deck later- that's what you'll be looking at when you paddle.
Though it is the hull which 'should' be smooth and the deck which need not be...funny hobby,this.....

Cheers
John