There is no FTP command for the CHMODing of files, so you really have to do it manually using ftp_exec(). I havn't tried this myself but I'm assuming it should work, but here is an example of what I would do.
//After we have connected to the FTP server
//and need to set the perms for a file/dir, use
if (ftp_exec($ftp_conn, 'chmod 0666 logs/log.txt'))
echo 'Successfully set permissions for logs/log.txt to 0666';
echo 'Failed to set permissions for logs/log.txt';
Again, I have not tested this, but I assume it would work. Hope that helps.