Hi,
If you use PDM to configure the PIX then, only alternate to configure the pix and avoid any conflict or loss of config is using CLI.
whatever you do via CLI, will be reflected in PDM, the next time you use it.
but with Cisco Secure Policy Manager or with Firewall MC, there is no way for them to know what has been changed manually (via CLI or via PDM), unless you do rediscover of the device.
Thanks
Nadeem