In the templates/main.dwt.php go to code view and place your cursor just before the </head>, then add the code you need to add.
I just tested this without an issue.
Your friends over here at WebAssist! These Dreamweaver extensions will assist you in building unlimited, custom websites.
These out-of-the-box solutions provide you proven, tested applications that can be up and running now. Build a store, a gallery, or a web-based email solution.