I know it's just a request, but it should stop most big search engines from crawling the wrong folders.FYI, robots.txt is merely a request to the web crawler(s). Most bots/crawlers will adhere to your requests in the txt file, but there are those bots that will ignore it.
In regards to your question, what you are saying is you have two domains like so:
Correct?
- example.com
- coolsites.com (which actually points to example.com/websites)
If this is the case, the robots.txt file that you have for the 1st domain will effect all sub directories (including example.com/websites).