Counteract rules are confusing. I understand the basic idea, but the way the rules are worded and organized leaves a lot to be desired. There also seems to be a missing rule for how the GM is supposed to determine the DC for anything other than an affliction or a spell.
Searching around on these forums, I have found a couple of other threads on this subject here and here. And the information in them is useful, but is somewhat disconnected.
What I am looking for here is the total process that you use for running a counteract check. I'll have mine here too. However, please don't just post corrections or critiques. Post your entire process that you use as well.
My process for counteract checks.
1) determine the counteract level of the target (the counteracted level). It runs on the scale of 1/2 level rounded up for everything except spells (because they already run on that scale). The level would be the character level of an ability, the spell level of a spell effect, a CR level of a monster or hazard or affliction, or an item level of an item.
2) determine the counteract level of the source initiating the counteract (the counteracting level). It also runs on the scale of 1/2 level rounded up for everything except spells. This follows the same determination as for the target's counteracted level.
3) determine the DC for the counteracted target. Afflictions and maybe some other things will list a counteract DC in their description. Spells use the spell DC of the caster that created the spell effect. For anything else(since the rules don't cover this), I usually use the DC by level table to set the DC.
4) determine the counteracting modifier for the source effect. For spells causing a counteract effect this is the spellcasting bonus (the proficiency modifier and relevant ability modifier). For skill counteract effects it would be the skill bonus (the rules don't really cover this either). In any case, the counteract modifier is also changed by any feats, abilities, or other such things that apply specifically to counteract checks (either generally to all counteract checks, or this specific type of counteract check).
5) Compare counteracting level against the counteracted level - remembering that these will only match what is printed for spells. For items, hazards, creature abilities, or practically anything else it will be 1/2 level rounded up.
6) make the roll. d20 + counteracting modifier vs counteracted DC. Determine level of success.
7) look up on the result table for the level of success rolled to see if the target is actually counteracted or not.