Cyclone IV GX starter Kit - PCIe

Before guiding you through the proper decoding of the BAR indication for received packets, I would question that you need two different BARs of equal kind for your different function’s tasks. Just split your BAR address range, say, the address range from 0x0000 to 0x0FFF is used for your first logic, then from 0x1000 to 0x1FFF for your second logic. You just have to decode the appropriate address wire. And your driver won’t mind either.