I agree with Shaun, you would have to balance each component seperately as, they all have different resonances. The crank would be balanced to '0' vibration, or what ever the measurment would be. Then the flywheel would have to be balanced to the same degree, to eliminate vibration. Then, providing the fit between the crank and flywheel is correct and true, you would'nt need to balance them further.
By balancing 1 component at a time, you're just reducing that parts contribution to vibration. Balancing just the flywheel would have a noticable effect on the overall feel of the engine, making it smoother in operation. However, that choice is a mutually exclusive one so, it doesn't necessitate the balancing of every other part !
Anyway you would definitely notice the difference a lightened flywheel would make to the engine response, regardless of whether it was balanced or not !