Uh, fsck -y won't fix file permissions, it's simply a disk utility that you can think of as a watered-down version of Norton Utilites. If you want to fix file permissions, boot off of the OS X install CD and open disk utility from the menu, somewhere in that app should be a button or something to fix file permissions.
But, if you still want to use fsck -y, reboot the computer, while its booting press and hold the Apple key, and the S key at the same time until you see text on a black background. Then wait for a prompt. There you type fsck -y, press enter, and wait for it to run. If it says that errors were fixed, run it again until it says the Hardrive is OK. Once your done, type 'exit' without the appostrophes and you'll be done. This doesn't fix permissions though.
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