In a large mixing bowl, combine warm water, yeast and sugar with half (3 cups) of the whole wheat flour. Whisk together and set aside for 10-15 minutes.
Add honey and salt to the yeast mixture and whisk. Add the remaining 3 cups of whole wheat flour and ap flour. Mix until the dough comes together.
Turn the dough out onto the counter and knead by hand for 8-10 minutes. Alternatively, you can us a stand mixer fitted with the dough hook attachments and mix on medium speed for 5-6 minutes.
Shape into two separate dough balls and place in greased 8.5 x 4.5 loaf pans.
Cover with a dry towel and let rise in a warm place for 30 minutes.
Bake at 375F for 35-40 minutes. Remove the loaves from their pans and allow to cool on a rack before slicing.