Larry,
We do not recommend operation of the system without all fans spinning. We have not performed any thermal validation with the chassis fans stopped and thus do not know whether all components will be properly protected in this situation.
Understand that, from an acoustics standpoint, it is actually possible that the system could be louder with the chassis fans stopped. Remember that the amount of airflow that is necessary through the CPU heatsink will increase if the air that is available is hotter (it's a poorer dissipater in that state). Since CPU fans are typically louder than chassis fans, the net result could be a louder system (depending upon thermal load as well, of course).
I also need to warn you that the SIO device that we use for fan speed control does not include a circuit to assist the fans in overcoming their inertia. Some fans will require the duty cycle to increase to a significant level before the fan will actually be able to start spinning. This could possibly mean that temperatures could rise to higher, more unsafe levels before the fans actually start spinning. This is less of an issue in newer systems; it is aged fans that have problems with inertia caused by dust buildup, etc.
If you wish to attempt to configure the system for operation in this state, you will need to modify the configuration in the Advanced Cooling scene. Clicking on the titles for the fans in the center of the scene will present the related parameters on the right-hand side of the scene. You will want to set the Minimum Duty Cycle from its default 30% down to 0. If you are utilizing the Intel(R) Desktop Utilities application, you will also want to change the Under-Speed Threshold from 250 RPM down to 0 so it doesn't generate alerts when the fan is stopped. Finally, because of the fan start issue, I would also recommend that you modify the configuration for the various temperature inputs to use the piece-wise linear or simple linear control algorithms, instead of the Proportion-Integral-Derivative (PID) algorithm, so that fan speed is increased at lower points on the thermal scale. Click on the titles for the temperature sensors in order to have the configuration parameters for these sensors displayed on the right-hand side of the scene.
...Scott