I usually just fill holes and cracks with standard wood filler, the kind you buy in a tube. There are enough varieties that I can colour match pretty easily. Filling cracks or holes doesn't add any strength, it's merely to facilitate the glass and epoxy, so there are no gaps where the glass won't be filled. The wood filler I use is very friendly, does not stain the hull, and sands off very easy. I found when I used thickened epoxy, it sanded off hard.
Usually people will wet out and fill with the same epoxy. My preferred method is to wet out with a very thin epoxy and fill with a thicker one. System three is great for this, as you can wet out with Clear coat, a very thin epoxy, and then fill with the general purpose epoxy. However, on my last few builds I have just used the same epoxy for wetting out and filing.
I'm not a believer in the seal coat, haven't noticed any difference on the many boats I have built.
I would only put the wet out coat on the inside of the canoe, no fill coats. Fill coats do not add strength, and the slightly textured feel of the glass on the inside can be helpful. Fill coats on the inside will add weight, and you will have to sand again.
Glassing the outside of the hull is actually one of the easiest parts of the entire build, and can be a very pleasant experience as you see the colours come to life.