There are two primary (and optional) configuration files:
All support files, including configuration files and templates, are contained in ${QNX_TARGET}/etc/system/config/pci/ on your development host, and are installed in /etc/system/config/pci/ on your target. You don't have to keep your configuration files there, but it does provide a consistent location.
The files pci_hw-template.cfg and pci_server-template.cfg contain a great amount of detail about their use.
When creating a custom configuration file, you can remove any sections or parameters that don't apply to your system. Removing the comments also helps to speed up the parsing. Just make sure not to delete any section tags for which you want to set a parameter, or it won't be interpreted. Empty sections are OK.