Moving projects and associated files around, Possible?

I was asked to work on a project for a add agency directly from their office, now the projects where saved on the boot up drive, it barely has space, i want to move the files unto a external drive but inside a proper folder structure i can understand, seems like FCP so far only saves files on a chosen scratch disk, is there a way to save the files on a disk and inside a folder?

Sure.  You can simply select a project in the Project Library area and choose File menu > Move Project, or File menu > Duplicate Project, depending on your specific needs.
http://help.apple.com/finalcutpro/mac/10.0/#ver4e2e1bd
http://help.apple.com/finalcutpro/mac/10.0/#verb6acba30

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