Installation of NopCommerce as application under a website

Im trying to run nopCommerce as an application under an already running website.

Basically we have an existing asp.net website for our E-commerce website and we want to move to NopCommerce. So i am trying to run the nopcommerce site as an application under the already running application.

So in IIS i have set the alias as nopcommerce. So the URL for my nopcommerce site becomes  'www.existingsite.co.uk/nopcommerce/'

I already have SSL enabled on the existing website and in my nopcommerce store setting I choose SSL enabled and set the secure url to 'https:www.existingsite.co.uk/nopcommerce/'

This throws the following warning in the warning pages.
Specified store URL (http://www.existingsite.co.uk/nopcommerce/) doesn't match this store URL (http://www.existingsite.co.uk/nopcommerce/nopcommerce/)

Most of the content on the site also doesnt appear because of this as the image/css/js files get an extra /nopcommerce appended. Not sure why this is the case. Can anybody shed light on this?