Use PCI avalon compiler in QSys.

Don't bother to mess with SOPC Builder together with QSys. The subtle difference in interfaces will give you too much trouble to deal with. In QSys, after you type pci in the libray search box, you'll find ip compiler for pci express usable for families before V generation. It is quite similar to pci compiler in SOPC Builder. For V generation, you have to use avalon-mm <family> hard ip for pcie Each component supports different feature set per family. Some porting work is required to move from one family to another. Not ideal, but you don't have to do it so often.