Can anyone tell me how can I update the header section or meta tags by using the main template page in dreamweaver cs4? 
Could you say a bit more about what you are doing / what your setup is? It’s better not to let Dw get too involved with your code, because you end up with problems like this which aren’t necessary if you deal with the code yourself. I’m not too familiar with these aspects of Dw, but if this is a section that’s reapeated on every page, it’s better to use something like a PHP include for that.