Since i was in the RAF i have had passports, well i lie, one before of course which was a South African one. On becoming an Aussie Okker, i took out an Aussie Passport as well, so had 2.
Used the Aus one t o depart when going to South Africa, then the SA one at SA Arrival, no troubles at all.
SA one out of SA, and Auas one on arrival back here.

Also used my Seamas ID Card a lot for travelling in the earlier days .
Still have Dual Citizenship, and both Passports, but have not used the SA one now for quite some time. The last Holiday with my Daughter to Cape Town in May last Year only used the Aus. One al the ways there and back.
Cheers