I have been researching this issue online because I want to be confident in the answer and haven't found a definitive explanation. I know the people here are the most knowledgeable around so here goes:

I have not booked tickets yet, but my plan is that my wife and I are flying BOS - DOH - JNB - VFA. I know the exact dates and times.
BOS throuh JNB is on Qatar. JNB - VFA is on Airlink which is a codeshare airline of Qatar.

My travel agent (who has been great and does everything except international travel arrangements) tells me to be sure I book the VFA flight on the same ticket. That way my baggage will be checked through from BOS to VFA. I have a 90 minute transfer in JNB and he says that is enough time, no problem, to make my connection IF I don't need to deal with baggage. If I do, it's going to be tight and there's a decent chance we, our bags, or both, don't make it.

However, I've been saving points for years for this special trip and I want to book award tickets. I can get BOS-DOH-JNB but then I will have to buy the final ticket using cash (can't use chase or avios on Airlink). Thus, we will be on seperate tickets.

I am wondering if, when I check in at Boston, I can show the two tickets - one being a Qatar award ticket (BOS-DOH-JNB) and the other being a $$-purchased Airlink - and have my bags checked through to VFA. There is some conflicting language about partner airlines and codeshares and baggage (Airlink is not oneworld).

My wife says not to risk it- it truly would severely damage our vacation itinerary to miss the VFA flight after a 90 min layover... there is no flight until the next day.

In my head, we would be flying business on award (qsuites for the first time!), and sounds great. We'd also be saving money (I'd be buying economy if paying cash). If it all works like I hope it might, I like this plan better. But I might be falling in love with wishful thinking.

Any advice? I'm even considering driving to BOS airport one of these days and talking to the counter, but I realize you might get different answers on different days depending on who you ask. I'm also considering calling Qatar and seeing if they can somehow link the two tickets if I buy one with award and one with cash.

I do have to travel with my wife for the next 14 days on vacation so keeping the peace is pretty valuable too