However i tested it out and it does not work, even though i get an email saying someone has made a comment, when i click on the link i get this message 'Can't find comment message. Maybe it has been deleted or unpublished by Administrator.'
It sounds like you've forgot to enable Autopublishing for guest's comments. By default all guest's comments are saved but not published - administrator should review them before publishing.
Also when you look at my front page, next to an article i see the 'jcomments ON', how can i fix that so that jcomments doesnt show on the front page like that?
In most cases you needn't to use {jcomments on} tag - just go to JComments' settings and select categories where comments should be enabled. After this comments would be enabled in all articles of selected categories.