I'm only running 2 GPUS per board until I get my riser cables, but didn't have to do anything to get cgminer to see both cards on each machine. try running this simple command to get started;
cgminer -o
http://pool:port -u username -p password
that should at least detect all the cards and mine on them
And, of course, "cgminer -n" will show you what cards cgminer detects.