Hi,
I explained you how the slideshow works. It is a "full-screen" slideshow. So, it is normal if the "website container" doesn't apply to it. Because it is "full-screen".
If you want to change the way how it looks; you would need some custom codings. It is a 100% custom modification and unfortunately we don't provide free support or step-by-step instructions for custom coding modifications.
You may purchase premium support:
www.flexiblewebdesign.com/premium-support
and let us take care this modification for you directly on your website though.
OR - use an another joomla slideshow module and publish it in "top" module position. There are many free slideshow modules free to download on extensions.joomla.org
Regards.
Support