There is no need to 'balance' each 120v circuit.
You should however have a valid distribution method, not fed from two 120v outlets, you should have an enclosure that distributes the 120- 0 -120v to each of the circuits, properly fused.
As to EMI filters on the VFD, the VFD has a natural filter immediately the supply enters it, this consists of a 3ph rectifier feeding a very large capacitor bank.
If using a ordinary 240v 3ph motor, you are better off to put the money into a 3ph choke on the VFD output.
It is best to consolidate everything in one enclosure rather than a mish-mash of separate devices hooked up.
BTW, when wiring, it is not code to use a wire gauge that has a larger fuse or protection than the conductor rating.
Al.