When it says affixes, it means you add the atk value added by your affixes (Soul, Modulator, Fever , Power/Shoot/Technique.......) they're separated from the weapon atk because they don't get the elemental multiplier, only the standard atk of the weapon gets affected by that, it's also the same for Black Heart potential or Slave potential , you will need to add their atk bonus in either "Affixes" or "Bare Handed ATP" otherwise they'll get a multiplier they're not supposed to get (the elemental value in this case).
Potential Ability is when the potential of the weapon gives a % boost to your Atk (such as Bio weapons, PA boost latent but for that one keep in mind your calculated dmg will concern only that PA). If a potential boosts your defense, no need to put the value, then there is the case of Black Heart and similar potentials i mentionned above.
In bare handed ATP you'll usually place the atk displayed between parenthesis (when you look for weapon requirement) then add your unit bonuses to it (affix + set effect) and nothing more (maybe Shifta boost if you know their exact value)
Hey, how exactly do you use that damage calculator thing? It's confusing me. When it says to add affixes, what does it mean? Just the attack of the combined affixes? And what do they mean by "Potential Ability?"