I seem to have 2 libraries one within another

I'm not sure how it got that way but possibly when I reinstalled windows and itunes then copied over the old library from an ext HDD.
Is there any way to fix it?  Do I need to fix it.  I prefer to have things as organized as possible.

Rebuilding your iPhoto library may help ...
iPhoto 6 and later: Rebuilding the iPhoto library

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