I am fairly sure that if your first flight is on CX then the online tool will send the booking to be ticketed by CX. This may not be ideal as your "home" airline seems to be AA.
Also the online tool has an ongoing problem whereby after you complete the booking and input your credit card info, you get the infamous 15012 error and have to start again. It's been happening for more than two years and had not been fixed as of late last year; don't know if it has been fixed this year?
In any case, I would definitely use the online tool to build and validate the booking, then call the ever-helpful AA RTW desk to book it and get the record locator. Then ticket it through the AA GSA in South Africa which I believe is still Mindpearl in Cape Town; they are familiar with the procedure.
Happy Travels.