I might caution against using an epoxy/wood dust mix. The reason is that it tends to make a pretty hard fill - much harder than the cedar around it. When you go to sand it to a flush, smooth shape it may be quite difficult to do so without dishing the cedar on either side of the fill. Epoxy mixtures made for hull fairing are generally phenolic microballoon mixtures, which are much easier to sand. You first coat the area with a thin coat of plain resin. Let it harden enough that it won't smear when you work on top of it and then mix your filler goop. The easiest to find may be a can of WEST System #407 low-density filler additive from places that sell marine supplies. You mix a small portion of your resin and hardener, stir them well and then start mixing in spoonfulls of filler powder. You want a mixture that is stiff enough to stand up without sagging and flowing (think peanut butter) and this is achieved with a lot of filler and a small amount of epoxy. If in doubt, add more filler as it is critical that this stuff holds it's shape, rather than start to run 15 minutes after you apply it. Overfill the area slightly using a spatula or stiff squeegee and let it harden. Once hardened for a couple of days (minimum) you sand it flush with a block of wood with some medium-grit sandpaper wrapped around it. With a filler of this density the task isn't too different in terms of smearing on the goo and later sanding it smooth, than filling a seam between two sheets of drywall in your kitchen.
This might be overkill, but I doubt the trench is actually very deep, which brings up another potential problem. The final, sanded fill won't be very thick and it will be crossing the seams between the planking. I'm not at all worried about the fills coming loose, but I am a bit worried about them cracking at the planking joints as the boat flexes and the planking moves. If it was my boat, I think I'd do my filling and fairing and then make small saw-cuts through the fill following the planking joints to allow more independent movement between the planks in the filled area.
Which brings up repair option #2: Whenever possible, the best filler for wood is often more wood. Not having seen the boat, I don't know how practical it is, but buying a 4'-5' long hunk of planking stock, cutting it into short chunks and glueing them into the depressions, plank by plank with epoxy resin might be possible. Once the epoxy hardened, they could be planed and sanded down flush and any additional filling done with a resin/filler mix.
