One question I do have is, are Disks/Partitions/(File System)/Folders/Files the exact same thing in Linux as it is in windows? Like for some reason I find that people will interchange the word Partition for the word Folder. For example, When I do an install it looks as though I have three partitions. Yet isn't /root a partiton also? Or does /root exist within "/" partition?
In Linux, the file system begins with / (root) and expands like an upside-down tree. Hard disk partitions can be mounted anywhere within that tree, and are usually mounted on directories specifically created to be used as mount points.

When you run the Knoppix installer, unless you manually change its configuration file, it installs itself completely on one hard disk partition, mounted as / (root). However, the books I've read often recommend using three or more hard disk partitions for Linux, usually /, /home, and /boot (so that if one of those partitions gets screwed up, the damage is limited to that one partition).

And of course there's the swap partition, which you can't "see" within Linux.

Say you have a Windows partition on hda1, and you mount it within Knoppix at /mnt/hda1. All /mnt/hda1 is, before you mount the Windows partition, is a directory you intend to use as a mount point. You could use it to store files. But as soon as you mounted the Windows partition on it, you'd no longer see the files you saved there...until you unmounted the Windows partition again.

You could theoretically mount the Windows partition to any directory you wanted to, but it would mess things up if you mounted it to the wrong one!

Your CD-ROM is (in Debian, at least) mounted at /cdrom, which again is just a regular directory before you actually mount your CD-ROM there.

(It's too bad Windows got people in the habit of using the term "folder" instead of "directories" and "subdirectories." Just makes things conceptually harder to understand IMHO.)