SA Citizens shows their SA Passport to enter and exit SA
Foreign Citizens has to enter SA with a Visa and passport.
Foreign Citizen with PR: Used to have a stamp in their passport to say they have PR, so they dont need to apply for a Visa each time to enter SA. However this is a very grey matter. Some use SA ID's with their passport and other uses their PR Original Certificate and some a certified copy of their PR (stamped in past 3 months by the SA Police). - This is one my wife uses.
SA took away the stamp for PR in their passport. They also said they wont replace lost PR certificates, which takes 2 years to replace (so 2 years where every bank always asks for it wont work).
A PR uses their foreign passport for travel by the way. When you have multiple citizenship ie my kids, they have a selection of 3 passports they can use. However to enter and exit SA they need to use their SA passport, to enter and exit Singapore they need their Singaporean passport, and so on. However go to Japan, they would use their Singaporean as its basically Visa free for them, whereas I use my South African one and have to apply for a Visa.
So basically you need to use your passport only entering and exiting the country it originates from, everywhere else, its upto you which is easier. Kids can have multiple citizenships up to the time of 18 then have to decide.