As I understand how things are usually done, a filler is applied directly to the raw canvas--filling in the weave to makeg for a smooth base for paint--followed by a few coats of paint, or perhaps primer and paint.
A high-build primer is intended to fill in very small scratches and other very small dings, and to be easi lysanded smooth. May be useful when dealing with an aold paint finish that has a bit of very fine paint cracking, though the risk there is that the paint may be getting ready to flack off.
I'm not sure how to approach a "dusty" filler -- but I think that if I had the surface basically smooth, I would try an oil-based primer, then a couple of coats of oil-based paint. If your surface still needs a bit a smoothing, a coat of high-build primer, sanding, and then primer and paint.
If the "dusty" filler is actually beginning the process of disintegrating, you may really have to replace the canvas. But since you've gone so far to prep the surface, there is little to be lost at this point by doing a final sanding/smoothing, and then priming and painting.
Some primers aren't much more than thinned paint, while others actually help with binding the paint to the surface -- and I don't know how to tell one from the other. If you have a good sound surface, priming is often not needed. But since you probably want to put a few coats of paint on, the first might as well be the primer for the paint you use.
Epiphanes is a brand of marine varnish and paint -- I have no experience myself with it, but it has a mixed reputaion on the WoodenBoat magazine forums, and I understand that, like most "marine" finishes, it is expensive.
Lots of folks on these forums, and some on the WoodenBoat forums, think the expense is needless, and that other good exterior grade paints do just fine on a canoe. Your dime, your call.
I guess this make it my 4 cents, now.