Multiple System Libraries

I have more than one "Library" folder, One in my SYSTEM folder and another in my USER folder. There are several of the same files in both. I'm wondering if in transferring from one laptop to another, restoring from backups as I replaced hard disks, upgrading from system to system, etc., if I mistakenly have created more than one.
Recently when I installed the latest Adobe Flash Player plugin and it didn't work, I placed another copy in the same location in the other library folder, and it did work. That made me wonder.
Question: Should I have multiple Library folders??
Can I consolidate to save space?
I'm afraid to do a clean install because for the most part, everything works........

Thanks for the feedback. BTW, get an ext HD large enough so you can put a bootable backup/clone of your *it works so good now* installation and keep it current. That way, you can always get back to that good state. It's especially important when installing updates. See these for details:
http://docs.info.apple.com/article.html?artnum=106941
http://www.macmaps.com/upgradefaq.html
http://www.macmaps.com/backup.html
http://www.thexlab.com/faqs/installswupdates.html
http://www.thexlab.com/faqs/backuprecovery.html

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