All secure files need to be uploaded to the /domains/domain.com/private_html directory. You may upload using the control panel's built-in file manager or FTP. For example,
/domains/domain.com/private_html/index.html ---> https://www.yourdomain.com/index.html
/domains/domain.com/private_html/secure/index.html ---> https://www.yourdomain.com/secure/index.html
The private_html directory operates the exact same way as the public_html directory.
Note: You will not see a private_html directory if the SSL feature isn't enabled on your account.