Have connected from QR to an Airlink flight a couple of times. I don't like my luggage being transferred in JNB from a security aspect so have always cleared customs and then rechecked in for the connecting flight (in my case one was Victoria Falls, the other Kasane in Botswana. There is a desk just past immigration where you can recheck your bags but there's often a line there. The easiest is to go to the Airlink check in counters which are extremely well staffed and efficient. If your ongoing flight is late morning/early afternoon the security line is not that busy and tends to be relatively fast.
If you're concerned you can book one of the meet and great services that will expedite immigration, check in and security for you but unless you have a tight connection you shouldn't have any issues.
If you have a full fare on a regional Airlink ticket you'll also have access to the Slow lounge which is one of the nicer lounges in JNB.