Place water, molasses, yeast, wheat flour, ground flax seed, bread flour, oat bran, rolled oats, amaranth seeds, and salt in the pan of a bread machine in the order recommended by manufacturer. Select dough cycle; press start and allow machine to run complete dough cycle.
Turn dough onto a lightly floured surface. Form dough into 2 loaves and place on baking stone. Cover loaves with a damp cloth and let rise until doubled in volume, about 1 hour.
Preheat oven to 375 degrees F (190 degrees C).
Bake in preheated oven until top is golden brown, 20 to 25 minutes. Slide loaf onto a work surface and gently tap bottom of loaf. If it sounds hollow, bread is done.