PC Device communication howto

First I'd get it all working using PIO transfers from the atom and software polling for completion.

You'll probably need that access to debug it all anyway - being able to hexdump on-chip memory/register areas is very useful.

You can then work on getting the fpga's PCIe master interface, and then dma to read/write host memory.

And also getting a 'completion' interrupt working.

If you are using a nios you should find it fairly simple to download code from the host (atom), that will be more productive than using JTAG.

But I agree with dwh, the pcie block ought to contain a simple dma transfer engine (feed avalon address, pcie address, count and press 'go').