SSL Certificate - Domain or Alias ?

I have a website up and running at mydomain.co.uk which works fine

I then set up a domain alias for the ecommerce aspect at shop.mydomain.co.uk, the ecommerce software is Zen Cart.

I obatined the SSL Certificate for the domain shop.mydomain and applied it changing the required settings in the configure.php files. When I go to https://shop.mydomain.co.uk although the contents of the site appear there are no graphics or formatting.

The graphics are shown by placeholders only if I click on the place holder the page reverts to http:// and displays ok.

However when I go to test the checkout it throws out an internal server error. If I reset the configure.php files back to how they were the checkout page will show up insecured but is otherwise fine

My question is should I have taken the SSL Certificate out for mydomain.co.uk as opposed to shop.mydomain.co.uk. The ecommerce is installed in a sub directory of mydomain.co.uk, with the domain alias ponting to that location

Apologies in advance if this is a basic question (I hope the above makes sense) but I am new to this and have not set up SSL before. Any help would be appreciated.

Hi,

You can secure the domain for which you have the SSL certificate.

Please submit a ticket at https://support.comodo.com/ with order# and error screenshot that will help us to serve you better.