I'm using the template tag polldaddy_get_rating_html() to put the post rating into a custom location and that works fine.
But it seems that the plugin will still insert code above or below your post/page/comment, even if you use the template tag. The rating will appear where your custom tag like it's supposed to, but there's unneccessary, duplicate code added.
Perhaps there could be an option in the admin for something like "Custom Placement" in addition to the 2 existing options of above or below the post. Same for pages and comments. And choosing that would remove the auto-insertion above or below posts.