Where do you suggest i put the pages directory that came with Link 2? should it be in the cgi-bin or should i put it in the entirely different html folder outside the cgi-bin?
Also how do I incorporate my own html code into pages. I'd like a completely different index page then link this to the categories I created with Links 2?

The pages should DEFINITELY be outside of the cgi-bin, some hosting companies configure the "cgi-bin" not to parse html documents, so you would get a 404 or 403 error message.

You should simply use the EXAMPLE directory structure that is listed in the README file.

Uh...EDIT the TEMPLATE files in the template directory.

Good luck!

Regards,

Eliot Lee