The harness we make is a generic harness, so the extra connectors in the injector harness will simply be left dangling if you go that route. You will specify the number of cylinders on the engine when you are calibrating it and the ECU will use this info for timing and fuel calculations. All 8 of the injector outputs will still fire, but you will only be using 6 of them.
Another option for you is to purchase the FAST system without a FAST harness and buy one of PTE's Buick specific harnesses.