A PCI bus bridge will normally have a set of registers that describe apertures of IO and memory space for use by devices on the far side of the bridge. Bus accesses that fall inside one of these apertures are forwarded to the other side of the bridge.
Your BIOS was smart enough to probe beyond the bridge, see the PD6729, and enable access to its IO registers... but the BIOS cannot know how to configure the PCI bridge to accommodate cards attached to the PD6729. So, pick a memory window to reserve for PCMCIA devices, program the bus bridge to match this window, and set up /etc/pcmcia/config.opts to use the same window. You will also probably need to set up or adjust the bridge's IO windows, and set appropriate IO port ranges in /etc/pcmcia/config.opts.
You'll need to get a datasheet for whichever bridge the PD6729 is attached to.