I have confused myself FAR more than I should on this, and am overthinking it. A branch called for help on a CTR - One check that is reportable, 2 payees, both present..

Obviously they are both listed, but would they both be "conducting on own behalf"? To me that makes it seem like two transactions... how can two people conduct one transaction. I think I am taking it too literal. Should we check one conducting and one benefiting? I guess it doesn't matter who, if so?

I think you report it with two part I entries, each checked in box 2a (conducting on own behalf). There's no rule limiting the number of individuals conducting the transaction. It's just that we almost always deal with one individual.