You could create a template called frontpage.php that will be your main page. Make sure it has this code at the top:
<?php /*
Template Name: Front
*/ ?>
Then create another template called footerhome.php. Place your floating javascript code there.
Return to your frontpage.php template file. At the bottom, instead of this:
<?php get_footer(); ?>
use this:
<?php include (TEMPLATEPATH . '/footerhome.php'); ?>
The frontpage.php file will load the footerhome.php file that contains your video code. The other template files will load the standard footer.php file.
Then create a new Page that will contain your main page contents. Make sure that the Page Template selected is "Front Page Template". It should appear in the dropdown after you've uploaded it to your theme's directory.
Now, in the WP dashboard, under Settings, Reading, make sure that under Front Page Displays... you check Static Page, and that the newly created Page is selected as what WordPress will display on the front page.
HTH.