After much searching, I found this little number http://extensions.joomla.org/extensions/site-management/seo-a-metadata/meta-data/5139
Just put your canonical tag in between these {tag}{/tag} and drop it in your article and it places it in the head of your page.
Bit long winded especially if you have the amount i had but it will hopefully get me by.
Thanks both
Ouji
