In general plan your safari routing in one flow like a circle, clockwise or counter clockwise. It feels natural and provides the best holiday experience. Avoid going back and forward and in zigzag. This feels uncomfortable and confusing. Let your African safari tour for example start in Johannesburg, move north east to Kruger, then further north to the Victoria Falls and from there to Cape Town. Depending on your international flight you might go back to Johannesburg or fly out directly from Cape Town. If for some reason you wish to start with Cape Town and the Cape Peninsula, maybe to recover from a long flight and to acclimatize, move then on to Kruger and further to the Victoria Falls and maybe also into Chobe and the Okavango Delta. Keep a close eye on flight connections to avoid “lost days” somewhere in the middle of your safari as they might take precious time you would rather like to spend in the bush.
An African safari circuit feels the best and will offer the best experience of a natural flow.