I've never found a way of doing it. So I just put in the first passport for the outbound sector, and then change it before checking-in for the inbound sector.

And if you forget, it's no big deal. For many destinations, OLCI requires you to re-enter the passport details at that time even if they have already been input as API, so it's a good prompt. Or the check-in desk will usually take a swipe of the passport. Somehow or other, they'll get the new details.