dare2, have you read the book?
You'll find tons of info on using WW flour there.
Yes, you absolutely can have WW flour in Phase 2. I use WW flour as a substitute for "all-purpose flour" in recipes and WW pastry flour (a.k.a. Whole Wheat White Flour) as a substitute for cake flour or when a recipe needs to be light and airy.
You might find a mix of the two works well. When using them, you may need to increase the moisture in your item to compensate or they will be a bit dry. Experiment.
I do this all the time (substitute WW flour and Splenda in baking recipes) and find that though it almost always works well, it works best in recipes that are meant to use that kind of hearty flavor, like apple crisps, oatmeal cookies, banana bread, etc.
Let us know how it goes!