Don't Make Me Count to Three is a wonderful book about raising children using heart-oriented discipline and the Word of God. I have loved it! It is along the lines of Shepherding a Child's Heart, but it gives many more examples of how to apply the ideas.
I also heartily recommend Wise Words for Moms. It is a REALLY HANDY chart that has bible verses to correspond with certain sins that your kids are prone to. BUT, a unique feature that is has is questions to probe your child's heart in each instance and help them to discern what is really going on in their heart.