Where are you adding the index page to - what folder? I presume you would have a folder named (with a shortended version of the secondsite.com name) ... that is where you would need to copy the index file into ...
If you can put up screenshots, then it would definitely be better - screenshots of your directory structure .. NOT the website
Ok - looking at the images, directory 1 (referring to the first image), you have two index files - one with an .html and another with .php extension - check which one your site is defaulting to.
Directory 2 (referring to your second image), has an index.php file only ... so, I'm assuming at this point, your server is not parsing the .php file then?
Do you have any .htaccess files (hidden) in either of those directories?
Also, HOW have you configured the domains names on your server?
It sure seems like it's uploading the page to the wrong location, however, I wonder why IF the secondary pages are being uploaded to the CORRECT directory on the server?
Have you looked on the server directly - either via SSH or some file manager on the server?
Ok - I am assuming you are setting your "Host directory" value (2nd image) under the FTP settings?
IF you are leaving them blank, then you DEFINITELY are uploading the pages (index) to the same primary (first site) directory .. and hence BOTH the sites look the same.