I’ve got German/Australian. I always enter and exit Australia on the Australian.
When I enter any other country I use the best one for the situation. Anywhere in Europe is German one obviously for example.
I think your question is more based on the fact that you were not sure if you have to use the same passport for the same flight. Is that right? That’s never the case. I’ve even been in Thailand on my Australian passport and done a visa run to KL and entered Malaysia with my German passport.