Say my main domain is www.domain1.com and then I make a folder at www.domain1.com/script/ . I buy a new domain called domain2.com and want to point it to domain1.com/script. When people view the domain and click a link will it appear is domain2.com/script/linkpage or domain2.com/linkpage?
With cPanel the process is far more simple when you buy and addon the domain through cPanel. Let cPanel create the directory. I did it the other way the first couple of times and was confused for years about how simple the process really is.