I use the check_by_ssh command to check remote linux machines disk usage. I created a check command called check_diskpath_by_ssh
command_line $USER1$/check_by_ssh -4 -t15 -i /keypath/keyfile -l support -H $HOSTNAME$ -C "/usr/lib/nagios/plugins/check_disk -w 15% -c 5% -p $ARG1$ --units GB"
The remote linux box must have the plugins installed in /usr/lib/nagios/plugins (or modify the command above). Notice the -p $ARG$ in the command above. That will allow you to pick a path to check. Here is a snippet from my service check:
That command will check the disk usage of the /opt path with a warning of 15% and a critical of 5% remaining free space. Adjust the percentages as you see fit. You will need to have separate service checks for each path for the host.