Computer system configuration resources include first and second control circuits in respective first and second integrated circuits. A communication link, which transfers data over a plurality of logical pipes, connects the two integrated circuits. Configuration of the link utilizes a link bridge that includes upstream (located closest to the CPU) configuration registers that are within the first control circuit and downstream ((located farthest from the CPU) configuration registers within the second control circuit. A link header, which includes upstream data for the first control circuit and down stream data for the second control circuit, is used to initialize the link. The upstream and downstream data may include information specifying the size of the communication link.