Looking at the product brief, it seems that the Intel CPU and the FPGA are being packaged on the same module and connected over PCI-E. So the interface from the

Looking at the product brief, it seems that the Intel CPU and the FPGA are being packaged on the same module and connected over PCI-E. So the interface from the processor to the FPGA will be over this connection. I imagine the development flow will be the same as if you connected these devices externally on your PCB. The processor won't need to know its connected to an FPGA, just a PCI-E device, and the same goes for the FPGA. The standard FPGA development flow can be followed.