I know that the Namibian War for Independence refers to the conflict between the South African Defence Force and SWAPO, and that the Angolan Civil War refers to the conflict between UNITA, FNLA, and the SADF on one side and the MPLA and Cuba on the other, but where does the Border War fit into all of this?
The South African Border War is a term that puts a focus on South African actions between 1966 and 1990. The overriding South African goals in this period were of (1) maintaining or installing a friendly government in Angola and (2) suppressing the SWAPO rebellion, both inside of Southwest Africa (Namibia) and in rear bases inside of Angola.
This time period from 1966-1990 includes 9 years (1966-1975) where the government of South Africa was working with the Portuguese Estado Novo in maintaining Portuguese control over Angola and resisting the efforts of MPLA, FNLA, and UNITA independence groups.
The following period from 1975-1990 covers the first fifteen years of the Angolan Civil War, with increasing South African material support for UNITA in exchange for for UNITA action against SWAPO bases in southern Angola. There were also periodic incursions into Angola by SADF forces on the hunt for SWAPO bases.
However, the Angolan Civil War covers a period from 1975 until 2002, with that first phase from 1975-1990 characterized by foreign intervention from South Africa and Cuba, driven by Cold War geopolitics. However, the second phase from 1990-2002 saw the withdrawal of South African and Western aid to UNITA after the Cold War, and a shift in UNITA behavior from being an anticommunist rebel group to 'warlord' rebels sustained by the mining of diamond and other mineral wealth.
The South African Border War and the Namibian War for Independence are much more easily compared. Both terms cover conflict between the SWAPO and the SADF between 1966 and 1990. Calling it the South African Border War would carry the implicit connotation that Southwest Africa was a part of South Africa, and the war was along the South African border with Angola (as well as including collateral actions supporting Portugal and later UNITA as part of the war), while calling it the Namibian War for Independence implicitly legitimizes the Southwest African Peoples Organization's claims that South African rule was illegal, and their struggle was one of national liberation.