The 7900 phones and the SPA9000 voice system are part of two separate voice solutions. As such, the 7900 phones will not participate in the auto-discovery and auto-configuration process use by the SPA9000 solution. Similarly, the SPA9000 wizard does not support the 7900 series phones. It may be technically possible to get the 7900s to register with the SPA9000 and make and receive calls, but it would require a lot of manual configuration work to set up, and you would not get the full functionality that you get if you use the SPA900 or SPA500 series of phones with the SPA9000. I'd recommend replacing the 7940 phones with SPA500 series phones in this case.
Cheers,
Dave.