If I essentially "turn off" a number of radiators by turning the adjustable vents to zero, how will this affect the whole system? I am doing this because some rooms on the second and third floor get too hot, or are not used much. Am I saving money by doing this, or just screwing everything up?
I do not think it will have much of a negative effect. But... if you are worried about it try timing a cold start in the morning with all the radiator vents open. time how long it takes to get steam to the end of the main vent then to the radiators. The next morning close the radiator vents and time it again. If the rooms warm up just as fast, then it had little effect.
A balanced system in which steam arrives at all the radiators at the same time is an economical system, which will save you money, especially if you keep a constant temperature.
It seems that your system has got out of balance, probably because of inadequate main (not radiator) venting.
Post some pictures of the boiler, and radiators, for further analysis.--NBC