Help with Two Document folders w/ same contents

Could use some help.......
I migrated from an older Mac to a new Mac about a month ago. At the same time I moved from Leopard to Snow Leopard. I used the Migration Assistant except for applications which I reinstalled from scratch (except preferences, etc. which were migrated).
In doing so I ended up, unbeknownst to me, with my documents both in the root level Documents folder ( /Documents) and in "my" user Documents folder (/Users/my/Documents). At least I assume that this happened during migration.
Today I found this out and, very unfortunately for me, that some of my Spotlight launches and subsequent file edits have not been to my Document files but to the duplicate ones at the root level.
I need to correct this, then delete those unwanted/unneeded duplicates and then block Spotlight from accessing that folder just in case something gets put there in the future.
With that as background my questions:
1. What are default post-install root (computer HD) level folders? Want to make sure no other errors. The folders I have are:
Applications
Desktop Folder
dev-1 (note: locked)
Documents
Library
System
User Guides and Information (note: alias)
Users
2. Is there an Apple utility or other way to compare this root level Documents folder with the users/my/Documents folder to determine what might have changed in the former when it should have been a change to the later?
3. Do those who use Spotlight frequently recommend privacy setting blocks beyond external drives? That has been my setting but now I feel I need to increase the privacy blocks.
Thank you in advance for any suggestions.

A Documents folder at the root may come from an old OS 9 system which did have a Documents folder at the root. In OS X your Documents folder is in the Home folder (Users/urshortname/Documents/.)
OS X has only the following root folders visible:
Applications
Library
System
Users
If you want to view the contents of the root level Documents folder just double-click on it to open a Finder window on the contents. There is no built-in folder comparison utility but there are third-party utilities you can find at VersionTracker or MacUpdate. Or just open a second window on the /Home/Documents/ folder and put them side by side.
I'm not sure I understand what you men by privacy blocks that you would need to create. Maybe you could clarify.

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