I would say part of the problem is you didn't change the right ones for the standard folders.
To do it right you need to change #3, 4, 5, 6, 162 icons
#3 and 4 would be the open folder like the one you used
#5 is the back #6 is the front and 162 is when you have folders within folders. In the screenshot below will show you some examples and they are all multilayered. You might be able to just change #3 and 4 but I am not sure. This tutorial may help you understand it better Folder Icon - Change Default Icon
Let me know if there's something you don't understand.