Complex sentence: The manor house (South Stoneham House) and parish church (St Mary) are in Swaythling, Southampton which was a second manor but which took over from South Stoneham in general use.
Split into simpler sentences: The manor house (South Stoneham House) and parish church (St Mary) are in Swaythling. Southampton was a second manor, but took over from South Stoneham as a name in general use.