Using SmartFTP, right click on the file you wish to modify in the server window. You should get the following menu:

Select Properties/CHMOD. This will bring up a "File Properties" window that should look like this:

Set the permissions for your .cgi file to what is shown.

Do NOT make .cgi scripts "Group" and "Public" writable!! Doing so will allow non-privileged users to update/modify your script.