SEO for subdomain and primary site
 

I have a travel related site which gets the contents from the Contents supplier. I set up a CNAME with my ISP and then we can access the pages from the subdomain, e.g. subdomain[dot]travelsite[dot]com/cruiseline1.htm

Now, I need suggestion on SEO for this site:

1. Do I need to treat it like two separate sites to do SEO? e.g. directory/SE submission
2. What is the best link structures between two sites?
3. Anything that I have to watch out?