If adding mix-ins like seeds, when would I do that? In the initial mix?

When I make seeded breads, I soak the seeds in water equal to their weight and add them, and the liquid, 30 minutes after stirring together the basic ingredients (the autolyse). This allows the gluten to begin forming, and also lets the flour to hydrate.
I've never tried this recipe, but I would caution you not to add a lot of seeds to the dough. I recently tested a no-knead whole wheat bread to which I added 2 tablespoons each of millet, flax seeds and toasted sesame seeds; its structure seemed particularly weak, which may also explain the minimal "oven spring" from baking. ;o)

I would add seeds, if you want them to be throughout the bread, in the initial mix.