Gives you root privledges
"r" is recursive (do all folders), "f" force
cp -rf /home/xyz /media/secondharddrive
Are the permission errors for YOUR home directory, as in you are trying to copy a file that is in use?
Can also look into rsync, which may work better (grsync is the GUI front-end).
Or you could try backing it up with Just-In-Time backup utility and then restore it to the new drive?
Oh, if you have any links/symlinks then that may mess things up. Try copying everything else. I got in trouble with my CrossOver and its recursive links to other parts of my /home directory.
Maybe try copying the non-hidden files and folders first, then unhide and go through the hidden folder one-at-a-time and see which ones are throwing you the error. You may not need that folder.