The darks in your underpainting look much too dark. You need to paint them a little lighter because when you glaze color into something that dark, you won't be able to see it.
Also, when you have such dark areas in the underpainting, there is no "room" to build light without creating extreme contrasts between light and shadow.
How to Paint Like the Old Masters has some flaws for sure, but it really helped me when I was learning to underpaint.