TS was correct (as usual :-)
Nikon CLS does let you manually control the settings of remote SB800, etc. In fact, it is flexible enough to allow one complete group to be TTL, another group to be manual. All lights within a group will be the same, either TTL or manual, you cannot mix within a group.
For the purposes described here, I concur that you would want to use manual controls in general. It is conceivable that you would want to light a large set manually, and then use TTL near camera, but if you use TTL at all, the preflashes will trigger any lights on slave mode. You would have to ensure that all non CLS lights are on radio triggers.
I highly recommend this book for Nikon Speedlight & CLS users. It has not to my knowledge been updated for the new SB700, but it does cover the menus/settings for the SB600, SB800, and SB900 (which differ from type to type). The menu steps to get CLS going on an SB600 are different than an SB800, etc.
http://www.amazon.com/Nikon-Creative-Lighting-System-Flashes/dp/1933952415/