how to edit a focus stacked image

Hi guys, a question about editing your focus stacked images (actualy about your in camera stacked images): do you edit each individual photo separately and then run them through the stacking software, or you edit only the final stacked jpg file? Sorry if this is a naive question, but I only recently discovered the world of focus stacking.

I use Linux, so I am a bit limited when it comes to software choices and tethering options although I am pretty confident with using Darktable to edit my "one shot" pictures, but I have no idea how to "correcty approach" the focus stacked photos.

Thanks for any tips.