I bake a lot in the breadmakers - as well as use them just on the dough cycle. I have a larger machine, up to 3 pound loaf.
At the end of the FINAL mixing/kneading/rising cycles - I pull the dough out of the pan, remove the paddles and slap it back into the pan.
At this point you should be able to feel the dough exhibit the "give" that should be there in a properly hydrated and correctly yeasted dough.
I don't like 100% whole wheat breads. They are too dense and do take longer to bake and I use bread flour for 1/4 of the total flour amount. I add vital wheat gluten and dried whole milk. And I add more yeast than the recipe specifies so the total is 1 1/2 times what would be right for a non whole wheat loaf.
I get great rise, a fine crumb and what I consider perfect crust.