Add the liquid ingredients (water, eggs, vinegar, oil) and salt and mix together
Add the fresh whole wheat flour and then the yeast.
Put the pan back in the bread machine and put it on the bread cycle – preferably whole wheat if your machine has this cycle.
As the dough is formed keep an eye on it to make sure that there is enough water. If the dough it too dry add water until it is somewhat sticky. An advantage of a bread machine is that you can work much more water into the dough than you would normally by hand. The whole grain flour tends to take longer to absorb the moisture so in the beginning aim to have it decidedly on the wet side.
Let the machine do its magic and return for a fresh whole grain loaf.