At the beginning of the study period, Southern Africa (South Africa, Botswana, Namibia, Zimbabwe, Lesotho, Swaziland) was inhabited by Khoisan peoples. By CE 1000, however, Bantu-speaking, iron-working, cattle-herding agriculturists had settled the region as far south as the Fish River, assimilating the native Khoisans. (Evidence for this contact is the retention of Khoisan clicks in many of the Bantu languages of the region.) The Kalahari Desert and the Cape Province, being poorly suited to Bantu-style agriculture, remained the domain of Khoisan nomads. Thus, if your ancestors were in southern Africa in CE 1490, it is safe to assume that their ancestors were also farther north in central and east Africa in earlier periods.
Although southern Africa has hosted many powerful kingdoms (such as the Rozvi Empire of Zimbabwe) and its people are highly mobile, we will limit our attention the really significant migrations. Seventeenth to eighteenth centuries - Dutch settlement : The first historic mass migration was prompted by the settlement of the Dutch at the Cape of Good Hope. Originally, this settlement was for the reprovisioning of Dutch ships bound for the Far East. Dutch agents traded with local Khoisan herders. When the herders were unwilling to trade as many animals as the Dutch needed, the latter responded by:
As soon as they arrived, the Dutch began marrying or otherwise fathering children with Khoisan women - the origin of the "colored" (i.e. mixed race) South Africans of the apartheid era. The Dutch were accompanied by slaves from West Africa and Angola. Thus, if your ancestors were South African "coloreds" in CE 1900 or 1800, their ancestors would have lived both in the Cape region, coastal west Africa, Angola, and in the Netherlands in CE 1490.
Early Eighteenth century - the Dutch meet the Bantus : The Dutch adapted well to the demands of semi-nomadic pastoralism, developing a mobile farming and herding Trekboer culture largely independent from the administration of the Cape colony and that competed with, but was rather similar to the cultures of the Xhosa people (Bantu pioneers) east of the Fish River. Indeed, some of the first contacts between Dutch and Xhosas seem to have been amorous, with pioneer trekboers marrying into and assimilating with Xhosa culture. It didn't last, however, as the two groups competed for the best farmland in a series of indecisive wars that lasted into the nineteenth century. By this point, the Dutch colonists were served by slaves taken from Khoisan and Bantu peoples. The inevitable result of the sexual aspects of slavery - more mixed race babies.
Early nineteenth century - "crushing" and "scattering": The consolidation of the Zulu kingdom resulted in a series of epic migrations alternately called the Mfecane ("crushing") or Difaqane ("scattering") depending on whether your people were taking it or dishing it out. It all started when the Nguni tribes of KwaZulu-Natal become the Zulu state: The Zulu state emerged from a series of epic struggles of two major clans - the Ndwandwes and the Mthethwas (helped by their junior allies, the Zulus). In this conflict the Mthethwas were defeated and dispersed, but regrouped under the brilliant leadership of Shaka, chief of the minor Zulu clan. The Zulus, taking up the Mthethwa cause, defeated the Ndwandwes and founded their powerful expansionist kingdom. (This was an incredible victory that places Shaka up there with history's most brilliant military leaders. At the time, Shaka's regiments probably contained the best disciplined soldiers in the world. Read about it some day.) The demographic results:
Late nineteenth century - colonialism: The discovery of the mineral wealth of northern South Africa caused the British to take the region more seriously, defeating and colonizing the Zulu kingdom and annexing the Boer republics. The mining industry completely transformed the region by:
Zimbabwe and Zambia, in turn, became the focus of mining companies with similar results. In other parts of southern Africa, colonialism followed the form established in East and Central Africa, with Namibia becoming a German colony and Botswana and Swaziland British.
Unlike with preindustrial settlers and locals, intermarriage between colonial officials and locals was rare but not completely unheard of. Your family folklore and the evidence of your senses will inform you.