As a relative new user I'm struggling with the same thing.
I calibrated the Z probe and set the offset with a G31 in config.g.
Now I start printing with PLA and babystep the first layer a couple tenths of microns until perfection is reached. I note the value and add it to my slicer offset for the next print. Next print I set the babystep value to 0 only to find out it doesn't work and re-adjust the offset and set it in my slicer. Rinse and repeat.
Change filament to PETG and find the same thing: confusion complete 
I also searched and found a lot on this topic but couldn't find a definitive answer on how the workflow is supposed to work?
I can add the offset to my G31 in config.g but this doesn't seem right since it's filament dependent. Would I add a "G30 H<offset>" to set the offset without actually probing the bed?
I could live with having a PLA/PETG specific offset in my (Prusa) slicer but I can't get it to work.
How do you guy's set this up?