I found this article to be helpful on how PCIe interacts with the CPU: http://xillybus.com/tutorials/pci-express-tlp-pcie-primer-tu...

PCI did for discovery, and could use it for device access (but often also memory-mapped). More info from the osdev wiki, which btw is a great place if you want to know about low-level initialization, the boot process etc.

http://wiki.osdev.org/PCI