It's not really a problem, you may need to extend the desktop onto the second GPU for it to be recognised through (if you haven't got a monitor connected),
another tip, install the Nvidia drivers first, the AMD second, i did have validitity problems with one app once (Both drivers at the time installed different versions of OpenCL.dll):
04/12/2013 21:25:07 | | Starting BOINC client version 7.2.33 for windows_x86_64
04/12/2013 21:25:07 | | log flags: file_xfer, sched_ops, task, coproc_debug, cpu_sched, dcf_debug
04/12/2013 21:25:07 | | log flags: sched_op_debug
04/12/2013 21:25:07 | | Libraries: libcurl/7.25.0 OpenSSL/1.0.1 zlib/1.2.6
04/12/2013 21:25:07 | | Data directory: C:\ProgramData\BOINC
04/12/2013 21:25:07 | | Running under account Claggy
04/12/2013 21:25:07 | | CUDA: NVIDIA GPU 0: GeForce GTX 460 (driver version 331.58, CUDA version 6.0, compute capability 2.1, 1024MB, 854MB available, 1075 GFLOPS peak)
04/12/2013 21:25:07 | | CAL: ATI GPU 0: AMD Radeon HD 7700 series (Capeverde) (CAL version 1.4.1848, 1024MB, 984MB available, 3584 GFLOPS peak)
04/12/2013 21:25:07 | | OpenCL: NVIDIA GPU 0: GeForce GTX 460 (driver version 331.58, device version OpenCL 1.1 CUDA, 1024MB, 854MB available, 1075 GFLOPS peak)
04/12/2013 21:25:07 | | OpenCL: AMD/ATI GPU 0: AMD Radeon HD 7700 series (Capeverde) (driver version 1348.4 (VM), device version OpenCL 1.2 AMD-APP (1348.4), 1024MB, 984MB available, 3584 GFLOPS peak)
04/12/2013 21:25:07 | | OpenCL CPU: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz (OpenCL driver vendor: Advanced Micro Devices, Inc., driver version 1348.4 (sse2,avx), device version OpenCL 1.2 AMD-APP (1348.4))
04/12/2013 21:25:07 | Collatz Conjecture | Found app_info.xml; using anonymous platform
04/12/2013 21:25:07 | SETI@home | Found app_info.xml; using anonymous platform
04/12/2013 21:25:07 | | Host name: P8Z68-V-Pro
04/12/2013 21:25:07 | | Processor: 8 GenuineIntel Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz [Family 6 Model 42 Stepping 7]
04/12/2013 21:25:07 | | Processor features: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss htt tm pni ssse3 cx16 sse4_1 sse4_2 popcnt aes syscall nx lm vmx tm2 pbe
04/12/2013 21:25:07 | | OS: Microsoft Windows 7: Home Premium x64 Edition, Service Pack 1, (06.01.7601.00)
04/12/2013 21:25:07 | | Memory: 7.98 GB physical, 15.95 GB virtual
04/12/2013 21:25:07 | | Disk: 1.82 TB total, 1.56 TB free
04/12/2013 21:25:07 | | Local time is UTC +0 hours
04/12/2013 21:25:07 | climateprediction.net | Found app_config.xml
04/12/2013 21:25:07 | Einstein@Home | Found app_config.xml
04/12/2013 21:25:07 | SETI@home | Found app_config.xml
04/12/2013 21:25:07 | SETI@home Beta Test | Found app_config.xml
04/12/2013 21:25:07 | PrimeGrid | Found app_config.xml
04/12/2013 21:25:07 | | Config: use all coprocessors
04/12/2013 21:25:07 | | Config: GUI RPCs allowed from:
04/12/2013 21:25:07 | | P5N-E-SLI
04/12/2013 21:25:07 | | SAMSUNG-R700
04/12/2013 21:25:07 | Albert@Home | URL http://albert.phys.uwm.edu/; Computer ID 8143; resource share 100
04/12/2013 21:25:07 | Collatz Conjecture | URL http://boinc.thesonntags.com/collatz/; Computer ID 20542; resource share 10
04/12/2013 21:25:07 | climateprediction.net | URL http://climateprediction.net/; Computer ID 1065924; resource share 20
04/12/2013 21:25:07 | Einstein@Home | URL http://einstein.phys.uwm.edu/; Computer ID 2542754; resource share 20
04/12/2013 21:25:07 | LHC@home 1.0 | URL http://lhcathomeclassic.cern.ch/sixtrack/; Computer ID 9967306; resource share 10
04/12/2013 21:25:07 | orbit@home | URL http://orbit.psi.edu/oah/; Computer ID 73849; resource share 10
04/12/2013 21:25:07 | Radioactive@Home | URL http://radioactiveathome.org/boinc/; Computer ID 5875; resource share 100
04/12/2013 21:25:07 | SETI@home | URL http://setiathome.berkeley.edu/; Computer ID 5427475; resource share 100
04/12/2013 21:25:07 | SETI@home Beta Test | URL http://setiweb.ssl.berkeley.edu/beta/; Computer ID 45274; resource share 100
04/12/2013 21:25:07 | PrimeGrid | URL http://www.primegrid.com/; Computer ID 224144; resource share 30
Claggy