As i cant know what app icons should have a pocket look or not and what icons you want at your dock you must make this manually:  

Dock icons:
This dock icons are normal smaller icons and must be named right and placed at the appropriate bundle folder of each app inside this theme.
For example:  Choose the icon "Messages.png", rename it to "icon@2x.png" and copy it to 
              Library/Themes/NoteBook.theme/Bundles/com.apple.MobileSMS/...here...  

Other Method: Make a copy of the icon, name both icons like on your springboard, one called "Messages@2x.png" and one "Messages.png" and copy both to the folder "Icons" inside the NoteBook.theme folder

This method isnt recomended because when you open the taskswitcher bar you can slightly see the orinal icon again above.
