Jacy,
When you check-in on BA does not affect your position in the onload list .. it is based on the priority we assign to your type of ticket and your date of joining / date of listing. You need to list in advance for all BA flights at idtravel.ba.com.
You must check-in using the self-service machines prior to going to the baggage drop.
If you are with American then rather than a simple ZED ticket you should be getting a ZED under the OneWorld agreement which will give you a higher priority on BA than non-OneWorld OAL staff.
CPT is normally a heavily booked route and so I would suggest that also get tickets on BA to/from JNB and then to/from JNB to CPT on Comair ( a BA subsidary covered by the BA interline agreement ).
In general BA will upgrade OAL if required ( rather than as a matter of course ) for them to travel rather than leave them behind but obviously our own staff come ahead on the list so with a popular route like CPT I would be surprised if you manage to get an upgrade but you can always hope...