You cannot use directory or files permissions if you have phpsuexec enabled - that's one of the security aspects of it. You'll have to work around it or go back to the less secure way of calling php.
The same as for phpsuexec, the CGI script must be chmod no higher that 755 and the directory that they're within should be no higher than 755.
I don't understand your upload question. You upload files as you always would do, via FTP. IF you still have old files that are owned by nobody:nobody you need to chown them under the root account to user:user instead.
I don't understand your upload question. You upload files as you always would do, via FTP. IF you still have old files that are owned by nobody:nobody you need to chown them under the root account to user:user instead.