Quartered arms could be one way for him to show that, yes. Although his eldest may or may not end up being the next Earl of Transha, given that KK has established that the tanistry of that clan isn't established by primogeniture but by clan choice of the most suitable heir to lead them, and she confirmed in chat a few months back that because of this, Dhugal might end up passing Cassan and Kierney on to his eldest son but Transha could end up going to a second or younger son. So in the generation following Dhugal, if there are two separate heirs, then they'd each inherit separate arms again, I would imagine.
As for Kelson granting Duncan arms that recognize both his Cassan heritage and his status in the Church, Duncan could have a similar mark of cadency to what I suggested earlier, only instead of a Ducal coronet, he could have a bishop's mitre in the central point. And as Elkhound mentioned, there would be a mitred crest in the total achievement anyway, though of course not on his fighting shield or the like unless the mitre were added as a charge on the device itself.