If you are using FTP via a command prompt, then you need to type something like
">chmod 755 [filename here]"
If you are using a GUI based tool to FTP, you either need one that will allow you to change file permissions, or you need to find out how to set file permissions in the tool you are using.
You upload the files first, then change the permissions.
How are you uploading files? Maybe someone else is using the same tool as you and can help, if you are not using the command prompt.