Jim, he's using Terragen 0.9.
You should be able to get full coverage by increasing Density Contrast and Density Shift. You should also turn on Clouds Cast Shadows in the Lighting Conditions window. You may also want to adjust Darkening in the Cloud Lighting Settings are of the Cloud Window. This should more or less give you the results you want (overcast).
The cloud layer saving functionality was never implemented. That's why it's grayed out. We have ceased development on Terragen 0.9 so if you want additional functionality you should try out the Terragen 2 Technology Preview, with greatly increased capability, including multiple cloud layers, saving of cloud layers, etc.
- Oshyan