Joomla and CS-Cart3

Hello, I have installed joomla into a sub folder ( of my CS-Cart website. I have links coming from CS-Cart to all different pages (support pages, blog, file downloads etc) in my Joomla site.

Is there anything i should be aware of working with two sites on one domain? Particularly when it comes to SEO.

One thing i did think about is the robots.txt. Should the content of the Joomla site be added to the CS-Cart robots.txt or will the search engines check both?


For information, search engines only check the root of a domain for the robots.txt file.