For the home page's canonical URL...
<link rel="canonical" href="http://mysite.com" />
OR
<link rel="canonical" href="http://mysite.com/" />
AND
Where should it be placed within the head section? at the top, somewhere in the middle, or last?
The rel="canonical" attribute should be used only to specify the preferred
version of many pages with identical content (although minor differences,
such as sort order, are okay).
That's from the Google description of the canonical
link. Therefore you shouldn't be using the site's root, therefore this question is moot.