Start by getting the PCI spec.... PCI22.pdf is usually easy to find on the net the 2.3 spec you will have to pay for.
Apart from that. Make sure that the IDSEL lines on the PCI connector is driven by DIFFERENT address lines. It sounds like your two slots use the same adress lines for IDSEL.
I'm having an issue with U-Boot failing to recognize PCI devices on
bootup. I have a CompactPCI chassis
with a PowerPC 405GP card and a Valleytech PCI carrier board with a TI
6415 DSP on it. The Valleytech
board has an Intel non-transparent PCI bridge chip on it. I also have
a PCI carrier board with two custom
mezzanine boards that have TI 6415 DSPs on them. We access the DSP PCI
interfaces directly on these
boards. My problem is that the PCI bus fails to find one of the boards
when both are plugged in at the
same time. If I only use the Valleytech board, I can talk to it fine;
conversely, if I only use our
custom, board, it works. When both are plugged in, U-Boot only lists
the card device ID for the card
furthest from the PPC. The PCI initialization also fails when I boot
the Debian kernel in this case. I
need to be able to access both cards at the same time so I need to
resolve this.