Baking with whole wheat flour--what is the difference?

I do a lot of baking for my kids, especially during the school year. Mostly cookies and quick breads or muffins. I want to start using whole wheat flour, but don’t want to ruin my reputation as a crafter of the world’s tastiest after-school snacks. Will substituting half the all-purpose flour with whole wheat flour have a noticeable effect on the taste?

Which kind of whole wheat flour is best suited for this kind of baking?

Any other tips you can share for baking with whole wheat flour and/or other substitutions for healthy baking? Thanks!