I'm not exactly sure what you mean. Site Options in SPD is where you can see/edit the elements the site designer automatically writes like the nav, footer etc. You can add javascript or other html to an element like "wh_title" but it will be in the body of the page.
There's a way to use the seo box to add scripts to the head but it has to be url encoded. If you want to add a script to the head, take a look at this - select "Verify your Office 365 site w/ search engines!" from the drop down on this page. Towards the bottom of the article you'll find "Adding javascripts to the -head- section."