Youtube video appearing on top of menu

It seems to do it on IE only as I looked at your site in other browsers. This happens to others and over the years, but you may want to read this:

http://www.jenkaufman.com/youtube-iframe-embed-video-problem-hides-menus-other-layers-546/

I would also recommend checking alternative ways of putting your videos in your page too instead of iframes (iframes are finicky).

You may also want to check this out
http://codex.wordpress.org/Embeds