Yep...when you use "dumb" radio triggers like the cowboys you describe, the remote flash is operated purely in manual mode, ie you have to adjust its output manually on the flash itself. The radio triggers are only used to tell the flash to fire at whatever the manually-set output is...there is no TTL or other fancy flash-metering going on with those triggers. You simply dial in the output you want on the flash and fire away.
Does this help?
For what it's worth, you can do the same thing (albeit via infrared transmission, not RF) with the D700 popup flash acting as commander and your sb600 configured as a remote. Consult your d700 manual for instructions on setting the popup flash as commander and your SB600 manual for instructions on operating it as an advanced wireless lighting remote.