How copy/backup home directory?

[buzst]

I'm trying to copy my home directory (using gnome) to my account on my server machine (which has the same name and is a member of the same group), many of the user and systems files don't copy (no error message) for what i suspect are permission problems. I don't want to change permissions on the system files so i'm thinking that I should create an archive of the directory and copy it to the server.

Is this the best way or is there a better way? If I create the achive in gnome will the system files that are being used go into the archive or do I need to become root and create the archive from the command line?

Thanks for the help