First off, welcome to v7n! 
#1. My advice is to not use DW's link update feature. It tends to get messy. When that little window appeared you should select ALL pages you want updated and then click on the Update links button. By just clicking the button without having a page selected will have no effect.
#2. You should be able to have your hierarchy as deep as you want, all that's required from you is to set the path correctly. Maybe if you can be more specific about your problem or maybe you can post here the code that doesn't work so we can have a look at it?
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...to be continued
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