Sealing every seam and joint on the ducts with duct mastic, caulking the register boots to the gypsum or subfloor, and taping the seams of the air handler will make the system operate as-designed. Both the supply and return ducts matter.
Closing off ducts (and returns) even partially lowers the overall operating efficiency of the system at the same time that it increases the heat load due to increased whole-house air infiltration, but it can remediate some balance problems.
If it's under-designed from a balance point of view you may have more serious tweaking to do. Sometimes it's easier to lower the heat load of the colder rooms rather than hack the heating system, but that's a more complicated call, and may not be very cheap. (Lowering the heat load of the colder rooms would have the least effect on the rest though.)