chmod sets file permissions. But you don't need exec to use it, as there's already a chmod() function in php. You can use crontab with exec to setup cron jobs.
Personally though, I wouldn't waste the time doing all this if you're only planning to move it once or twice. It will take a lot longer to set up all the automation scripts and debug it then it would to just ftp in, set the permissions, and do the cronjobs in cpanel. Of course if it's something you're going to redistribute then that's another story.