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You copy the old files back - its the opposite to how you did the first backup. Follow the instructions for your backup utility.
Most config files end up in /etc though user configuration files are in the home directory: they start with a dot
"system configuration" is a broad term though - for instance, the initial ramdisk and the kernel are in /boot - these contain configuration things too.
So you need to think about exactly what you want to get back - some of the configuration may not be appropriate.
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