This is the recipe I have been using for several years. For the bigger machine I doubled the recipe. (Oster)
After the three kneading cycles I pull the dough out, cut off about one-third which goes into an oiled plastic bag and into the fridge.
I sort of reshape the remaining dough and after removing the paddles, slap it back into the machine for the final rise and bake.
The original recipe works fine in a 2-pound machine - I have several machine and use the smaller one occasionally.
I looked up my notes and for the regular sized loaf, I used 2 1/2 cups of whole wheat flour and 1 cup of bread flour.
I used TWO rounded teaspoons of yeast. 2 rounded teaspoons of vital wheat gluten and 2 rounded tablespoons of whole milk powder - You can order it from King Arthur but if you have a market that carries Hispanic foods, they carry a product called "Nido" which is whole milk powder. The regular supermarkets around here don't carry it but the Mexican supermarket does.
http://www.kingarthurflour.com/recipes/100-whole-wheat-bread-for-the-bread-machine-recipe