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The live usb won't touch your original built in drive, unless you tell it to, with install / upgrade features... once you are booted up off the live cd, you can check and make sure it detected and mounted your custom partitions, and if not, you can mount them manually before proceeding with installs / upgrades. From my reckoning, they would have to be in the live-cd's fstab to automount, so you will probably have to mount them manually.
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