cp: omitting directory ‘/home/user/’

That happens because you did not use the option --recursive (-r):
$ cp -r /home/user /computer/media/user/TOSHIBA

But you had actually better use option --archive (-a):
$ cp -a /home/user /computer/media/user/TOSHIBA

'info cp' explains those options:
`-a'
`--archive'
     Preserve as much as possible of the structure and attributes of the
     original files in the copy (but do not attempt to preserve internal
     directory structure; i.e., `ls -U' may list the entries in a copied
     directory in a different order).  Try to preserve SELinux security
     context and extended attributes (xattr), but ignore any failure to
     do that and print no corresponding diagnostic.  Equivalent to `-dR
     --preserve=all' with the reduced diagnostics.
`-R'
`-r'
`--recursive'
     Copy directories recursively.  By default, do not follow symbolic
     links in the source; see the `--archive' (`-a'), `-d',
     `--dereference' (`-L'), `--no-dereference' (`-P'), and `-H'
     options.  Special files are copied by creating a destination file
     of the same type as the source; see the `--copy-contents' option.
     It is not portable to use `-r' to copy symbolic links or special
     files.  On some non-GNU systems, `-r' implies the equivalent of
     `-L' and `--copy-contents' for historical reasons.  Also, it is
     not portable to use `-R' to copy symbolic links unless you also
     specify `-P', as POSIX allows implementations that dereference
     symbolic links by default.

I got a credit card sized usb "device" (or "mock device") with my FSF membership that says "GNU/Linux Inside!" and I've plugged this credit card into several computers and got nothing.

This is a Live Trisquel system (including the installer)! Once plugged, you must reboot on the USB key. Some key pressed right after the computers powers up may provides you boot options, otherwise configure the boot order in the BIOS/UEFI so that the USB key has precedence over the hard drive. Like lembas wrote, you can backup from the Live system using its graphical file manager (the partitions on the internal and external hard drives will be icons on the desktop). After that, another icon proposes you to install Trisquel. Unmount and unplug the external hard drive first so that you do not install Trisquel on it by mistake!

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