Thanks, that clears it up for me. Based on this information, I should be able to simply leave the D800 in Commander Mode, even when I've got an SB-800 attached to the hot shoe. If I want to use the SB-800 as a TTL flash, then all I need to do is make sure that the SB-800 is in TTL or TTL-BL mode. I won't need to make any changes to the D800 via the menu.
This is very convenient as I often switch between using the onboard flash to trigger other flashes via CLS, and having a SB-800 in the hot shoe, or connected via my SC-17 cord. No menu changes necessary.
Thanks again for responding and answering my questions.