Hi. Iso-Cups w/Hi-End Base and Lampblack Ball are configured as pictured:

The component sits directly on the lampblack ball, the Iso-Cup w/stainless steel Hi-End Base sits directly on the shelf. So the configuration is:
Amp
I
lampblack ball
I
Iso-Cup
I
hi-end base
I
rack shelf
(An information sheet accompanies the product and should answer any questions about setup and arrangement.)
This is the standard arrangement. You can experiment with other configurations, such as the one you are using, or use the Iso-Cups upside-down. You'll get slightly different results with different configurations. The standard is most stable and gives best sonic results in most circumstances.
Edit 12/13/2011: Frosted Clear Iso-Cup has been replaced in our product lineup with a newly-formulated black Iso-Cup and SuperSonic Hardball. The new Iso-Cup achieves a sonic result equal to or better than the Clear Iso-Cup w/Lampblack Ball + Hi-End Base, without needing the Hi-End Base.
Iso-Cup w/SuperSonic Hardball Steve
Herbie's Audio Lab