You cannot use server side scripts such as includes, ASP, PHP, etc.
To add a script, do the following:
Login to your website administration.
Click on the Website Settings icon.
Find the section: Custom Header-Footer Script/HTML/Text.
Then in the text box labeled: "Website Header is ran between the <head> tags."
Paste your script or code.
Click "Save Changes" located at the bottom of the webpage.
Note: Anything pasted into this textbox will appear on all your websites pages, not just the home page.