The amperage draw should not be different, or at least should be minimal. For example if the motor is a three phase 5HP 575V motor the nameplate amps will be roughly 5A. It will vary slightly from motor to motor. All 3 phases should draw within 3% or so of each other: 4.8, 4.9, 4.75. Overload protection and fusing are not the same and BOTH should be used. Overload should be set at, or slightly above, the nameplate amps. The fuses should be 175% higher. Overload protects the motor, fuses protects the line.
Your amperage draw should have a minimal difference between the phases, not enough to require different overload protection. If there is significant difference you either have a motor problem or a supply issue. Start with the supply make sure the voltage is the same in all phases.