I use to have my template on the root folder, this will control all the page on web/mysite/www
Now I want to move the template to web/mysite/www/templates.
I did move it but all the pages that were linked to that website are looking at the template at the old root, how can I fix this???
The Templates folder must be in the ROOT level of the site. Always. As long as that is the case, they will always be found by the root relative link in the head of each child page.
However, your question is a bit vague and confusing.