Ok, I have been heavily modifying the site_html.pl file, and ended up inserting the header and footer code into the site_html.pl myself because I could not get it print out correctly otherwise.
Having done this the meta tags entered in the Links Managers no longer print out into the individual pages and catagories.
I was wondering if anyone could tell me what command(s) I would need to enter just below the <title> command in the html within site_html.pl to have the meta tags printed into the pages during building?
Any help will get you my never ending thanks. =)

   
I got it! Nevermind... the answer was as simple as scanning the file very closely until I found the commands and then inserting them into the html. Doh!