Have a look at this:
"After configurations are deployed, you should make changes only through Security Manager for configurations that Security Manager controls. This varies based on operating system:
•ASA, PIX, FWSM, IPS operating systems-Security Manager controls the entire configuration. You should make all changes through Security Manager.
•IOS Software-You have more control over which aspects of the device configuration Security Manager controls. If you do not create policies for a feature in Security Manager, such as routing policies, Security Manager does not control those features on the device. If you do create policies for these features, Security Manager overwrites the settings on the device with the settings you defined in Security Manager. Through administration settings, you can control the types of policies that will be available for IOS devices, thereby preventing Security Manager from displaying or changing policies for these features. To see the available features for IOS routers and control whether they are available for management in Security Manager, select Tools > Security Manager Administration, then select Policy Management. For IOS devices, Security Manager does manage VPN-related policies. "
http://www.cisco.com/en/US/docs/security/security_management/cisco_security_manager/security_manager/3.2.1/user/guide/dpman.html#wp307170
Regards
Farrukh
