Keep the bigger harmonic balancer on the new engine as long as the timing pointer is also included with the new one. I assume you are running a manual transmission, probably best to keep the flywheel/clutch assy. from the old set-up. Are you SURE that they are both 350's, I ask this only because all of the small blocks have interchangeable flywheels and balancers EXCEPT the small block 400 which is externally balanced with a flywheel and balancer all it's own. While you are in the process are you replacing the front and rear crankshaft seals?

1957 Chevrolet 5700 LCF 283 SM420 2 speed rear, 1955 IH 300U T/A, 1978 Corvette 350 auto, 1978 Yamaha DT175, 1999 Harley Davidson Softail Fat Boy