For example, if I wanted to do it with Merrill's yummy cookie recipe from earlier this week. I had a cookie with WW flour recently and it was yum so I am interested in trying it out.
I've always heard 1/3 WW to 2/3 AP is the best ratio.
When I want to make whole grain cookies, I substitute equal amounts of King Arthur white whole wheat flour. It's ground finer than most regular whole wheat flour, so results will be similar to AP flour when making cookies.
I also do a straight switch if using white whole wheat or whole wheat pastry flour. For great, great whole grain baking, if you haven't already, check out Kim Boyce's Good to the Grain.