Series will add the voltage, parallel will add the amp hours and discharge rate. For the VESC higher voltages are definitely recommended depending on your kV, and hub motors generally have issues with heat dissipation so raising the voltage should lower the amps and heat, however how heat in a motor is generated seems to be debatable.
In series you would have 12S * 3Ah = 133.2Wh with 20C discharge and in parallel you would have 6S * 6Ah = 133.2Wh with a 40C discharge rate. Since lipos are capable of discharging high currents they generally do not need to be wired in parallel, your pack in series should be capable of 60A continuous and 120 in parallel. Li-ion packs need to have cells in parallel since their discharge rates are much lower (eg. 20A continuous for Samsung 25R cells).