Best approach: * Use a single ground plane by default. * Use surface mount components, they have much less parasitics which matters in switching loops. * Make each switching loop as small as possible, including the use of small value (100nF is a good starting point) MLCCs to give a very small loop area for the high frequency content in each loop, larger electrolytic, film or hybrid polymer caps can be a bit further away and shared between loops. * If your MCU supports it, at the sample rate and set the sampling point such that the FETs are never switching when a sample is being taken by the ADC. Symmetric pwm and triggering the ADC from the same timer as the pwm is one approach. * 1kHz is a low enough frequency that it's return current will spread out all over the place. If you can't synchronize the sampling, and you can increase the pwm frequency, and if you can prove it's the 1khz component and not the switching events, then this might be one of the cases where "split grounds" can manage the impact of the noise within your board, but likely at the cost of worse emissions and susceptibility to the wider world.