Some thouhts:
One way to deal with low spots is to sand the high spots down so that you have a smooth surface. As long as the high spots aren't really high, so that your strips will be too thin, I think that's the way to go. A random orbit sander with 80 grit paper will do the initial job, and then work up to 180 or 220 grit, and if your sanding cedar, it will go pretty quickly. In fact, make sure you don't remove to much wood or create flat spots. Nick recommends using a long flexible fairing sander to remove high spots. You'll be surprised how a little sanding will make those uneven strips look great.
I agree that I wouldn't fill those low spots with resin and filler...that would look pretty ugly, I think.
I just double checked Nick's book, "Building Strip Planked Boats," and on page 151 and the next few pages he covers fill coats.
A good time to apply a fill coat is when a cotton ball sticks to it. This will give you a good chemical bond. With average temperature and slow hardener, that's usually from one to two hours after your first coat. Nick writes that he often does his fill coat the next morning and that way the resin is still green. So You can put on a fill coat (without sanding before hand) up until the time a thumbnail does not make an impression on the resin. After that, you need to do a light sanding to give your fill coat mechanical adhesion. You can use a kitchen scrubber or fine sandpaper, and the point is to just rough up the surface, not to sand everything down.
You'll want a second fill coat to the point that the resin can be sanded smooth without sanding into the glass fiber, which would reduce your strength, but not so much resin that you're adding unnecessary weight.
It's worth reading the MAS web site fiberglass FAQ at:
http://www.masepoxies.com/Epoxy_School_/Tech_Support_FAQ.html
After your final resin coat passes the thumbnail test, you can sand it smooth to 220 or 320 grit level. If you start cutting into glass fiber, you need to recoat with resin. Oh, and use a respirator, gloves, long sleeved shirt, hat, etc. when sanding. You really do not want to breate that stuff or get it embedded in your skin.
After you finish sanding, you'll want to let your resin cure a bit before varnishing. There's a variety of opinion on how long to wait. Note the chart on the MAS FAQ chart on curing. The main influences on curing is temperature and whether you use fast, medium or slow hardener. Given it's late summer, you probably should stick to slow hardener, and that's what CLC ships. With hot summer weather, your resin may be cured in a couple of days.
Get a good spar varnish that has UV protection, which is the reason you varnish. Otherwise, the sun will screw up your fiberglass and resin after a few years. There's lots of thoughts from various builders as to the best varnish. Some people also recommend going to an auto paint shop and getting a clear coat, but that's more expensive.
Avoid sanding your resin in the morning and then varnishing in the heat of the day. The heat will evaporate your resin before it can spread out in to a smooth layer. Better to sand and then varnish in the cool of the morning, between 60 and 80 F. Avoid doing it on a day when there's rain in the forecast. Be patient.
I recommend Nick's book. He covers all this in depth.
Good luck.