Have you tried using --gpu-reorder to have cgminer sort the GPUs by PCI bus? This may or may not be helpful depending on how the motherboard's buses are numbered... but I think they are supposed to be numbered geographically starting at the CPU and moving away from it. (Please correct me if I'm wrong.)
I don't know a whole lot about Linux, but there are some Linux hardware monitors that may be helpful:
http://alternativeto.net/software/gpu-z/?platform=linuxIf you get a good hardware monitor and --gpu-reorder alone isn't helpful, you can enable one GPU at a time in cgminer and watch the temperatures and clock speeds in the hardware monitor to determine which GPU is mining. Although this may only be helpful if the hardware monitor provides enough information to identify which physical GPU is which displayed GPU.
As a last resort, you could enable one GPU at a time in cgminer and try to actually watch the fans on the GPUs to see which one is running at 100% (assuming you have cgminer set to control fan speed accordingly). I haven't tried this so I can't say for sure it will be possible, but I'm guessing with six GPUs you don't have them all mounted inside the case so you may be able to see or hear the one running at 100%.
Perhaps using it with the information here:
http://superuser.com/questions/117239/how-can-i-get-multiple-video-cards-to-work-on-linux would be helpful? Again, not a Linux user so I may not know what I'm talking about... but since nobody has replied yet I figured I'd try to help.
