In this set up you will be able to use hardware decoding/encoding with Media SDK just fine. The only detail you need to care of is to request the appropriate implementation type of Media SDK library in MFXInit call. For example you can use MFX_IMPL_HARDWARE_ANY (Find the platform-specific implementation on any display adapter including the default display adapter).For more detail please check out MFXImpl enumerator in the Media SDK reference manual (the file mediasdk_man.pdf under \doc).
What I meant to say was that it is possible to get hardware acceleration through Media SDK if Intel Graphics is not the primary adapter in the system. But it must be active i.e. connected to a display.
As for GPGPU operation with Intel OpenCL SDK I'm afraid it's not yet possible as Alpha OpenCL SDK supports only CPU devices. So I would assume it is a bit early to speak of how it will work in multi-monitor setting.