set thumbnail as custom field

The URL is saved to the “_video_thumbnail” custom field. This can be changed near the beginning of video-thumbnails.php in this line:

define( 'VIDEO_THUMBNAILS_FIELD', '_video_thumbnail' );

Disclaimer: I don’t recommend doing this because I can’t guarantee it will work, you’ll have to change it again after every plugin update, and it might not always be possible to change this easily. But if you don’t have any other option it’s worth a shot. Also, good themes should be using post thumbnails and custom image sizes instead of timthumb.