Well, to start off with, when you first install fedora, you can put all those system folders into their own partitions. I guess if your running a server that might make more sense. On the desktop, less.
If you have room on your hard disk, you can copy the folders to the free partitions, then change the lines in fstab that point to those folders, and point them to the new partition. This will mount these folders as the computer boots up. Linux looks at everything as a file/folder. Moving that file/folder is as easy as changing how it's pointed to in fstab.

Try looking at "man fstab" to see how it works