When you use the OBiTALK portal to configure your device, it's an all-or-nothing thing. My suggestion is that you have an "advanced" section that would list all of the configuration pages found in the device and have a checkbox next to each, that you could uncheck if you do not want the portal to configure that page. So, for example, you could have the portal configure your SP1 settings but not your SP2 settings.
In time you could make it even more granular, to allow exclusion of certain sections within a configuration page, or even in some cases individual settings (perhaps allowing you to enter your "custom" settings in the portal, so they would be written instead of any default configuration). But to start with, the ability to exclude pages from configuration would be most helpful.