I agree with Dave on QSYS.
I have run the Stratix V Kit card running several designs with DMA and NIOS .... I am currently working with Arria V and Cyclone IV kit cards.
Possibly I can go back to see if I have something that worked on Stratix V.
From my experience the main issue was developing a Linux DD for the application I had since I was focused on Linux systems.
If you are in the Windows world, there is some support for PCIe drivers in the examples.
I have found 3 problems related to execution ...
1. The documentation is good but as you indicate somewhat scrambled on how to find it . There needs to be a more intelligent search engine maybe within
Altera to generate results based on the documentation out there.
2. On the kits and example applications, it seems there are sample applications but often they need conversion to the FPGA family of interest.
Also, the kits may have been developed including BTS and examples with a previous development system and now QSYS seems to be they way and
I can't easily run the examples that came with the kit.
3. For PCIe , the HARD IP core is configured as a Megafunction or similar and I have not been successful in running the Megafunction editor or PCIe
IP compiler to fine tune the IP.
Best Regards, Bob.