You can use command line or ftp client.
Yes, after installation you must change the permissions of these files. Do it with command line or ftp client.
Path are usually:
where kontrolpanel is your custom admin directory.
Change directory and set permissions:
chmod 600 web/includes/configure.php
chmod 600 web/kontrolpanel/includes/configure.php
Using 600 is the best choice in this case (only for the config files).
Address for the database means where the database is located. If your mysql server is running in the same server just use localhost
Website settings. php mode: Choose fastcgi, version default and enable suexec. Disable CGI, SSI, Perl, Ruby and python