How to work with the notch filter?

I would suggest that you set your Notch to 40 dB attenuation when simply filtering out noise. The attenuation is there primarily for use in the fixed notch when dealing with frame harmonic or dampening issues.

Iā€™ve applied the notch filter on a new build, and looking at a log of motor outputs they are definitely smoother then pre-filter.
But then I ran autotune, and it took longer then expected. Should I have had run an autotune before the FFT logging ?

I donā€™t think you need to if you are already flying, although I suppose if you are running the dynamic harmonic notch then a good tune before might make your ref value estimate more accurate. I donā€™t think the time it takes means much - I have seen 25% variability in the tune and thatā€™s apparently expected. Note that for a really good tune at hover to be truly effective you really need to get the thrust linearization correct which means setting MOT_THST_EXPO correctly - and changing it will affect your tune, hover thrust and therefore ref value. Even then @Leonardthall gets really good values for the notch center for large copters whereas I see quite a lot of divergence at high throttle for smaller copters.