At the bottom of the index.php file in the plugin is this code:
$args['post_type'] = 'page';
new kdMultipleFeaturedImages( $args );
You would need to replicate that, but with a different post-type instead of "page".
So you'd copy the two lines and paste them below, but change where it says "page".
This is a hacky way of doing it, but it should work. You may also want to change the plugin folder name and the name at the top of the index.php file, to avoid WordPress asking you to upgrade it (which would wipe out your changes).
You may also be able to hook in at init and add it via a theme or plugin there, but I'm not certain. I'm also not promising that would work in future versions either, as I may modify the way that part of the plugin works in future as it doesn't look like I did a particular great job of it originally (ie: it doesn't let you easily add custom post-types in it's current form).