There seems to be only one set of files
There would only be one set of files if you started off without SSL, and all the files in a folder called httpdocs or similar. What schoolboy is saying is that some hosts use an antiquated system where SSL files have to be located in another folder, usually called httpsdocs or similar. This means that you have to upload all files in the httpdocs folder to the new httpsdocs folder, and when you edit one file you have to edit both to keep them in sync.

Files should have permissions of 644, except for the two configure.php files which should have permissions of 644, 444 or 400 (depending on the server configuration). Files should never have permissions of 777.

Vger