The SIXAXIS controller communicates wirelessly the PS3 via Bluetooth.
See Pascal's page for details on getting things working.
At poweron, the Sixaxis will connect to the paired host on L2CAP PSM 17 and 19. Rather than going through the kernel's HID stack and input layer, you can just listen for connections on these PSMs yourself and process the data. For an example of how to do this from C, see server.tar.gz.