On the PCI bus, the BIOS (or Linux) assigns IRQs (interrupts) so as to avoid conflicts with the IRQs it knows about on the ISA bus. Sometimes the CMOS BIOS menu may allow one to assign IRQs to PCI cards or to tell the BIOS what IRQs are to be reserved for ISA devices. The assignments are known as a "routing table". In MS Windows it's called "IRQ steering" but this also covers the case of dynamic IRQ routing after boot-time. The BIOS may support it's own IRQ steering.
You might think that since the PCI is using IRQs (designed for the ISA bus) it might be slow since the ISA bus was slow. Not really. The ISA Interrupt Controller Chip(s) has a direct interrupt wire going to the CPU so it can get immediate attention. While signals on the old ISA address and data buses are slow to get to the CPU, the IRQ interrupt signals get there very fast. The ACPI even has a narrow bus going directly to the CPU.
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