Im wanting to create daily backups of all my accounts mysql databases, i.e :

all mysql db's on www mt2.fs-uk.com & www hns.fs-uk.com

will be backed up and stored in www fs-uk.com/backups/mysql

Is there anyway to do this either by running a cron job on each account or any other way?

Any help is much appreciated.

http://sourceforge.net/projects/automysqlbackup/

You seem to be running cpanel. Do you own the server or is just on a shared plan?