CS pins has nothing to do with hardware defined SS pin.
You should define the CS pin for each SPI slave in the code and It is your responsibility to ensure that these pins are switched correctly.
The SPI library itself does not know anything about the fact that it has many slaves; it always works with only one. You switch CS pins in the code and thereby control which slave will respond to the master’s requests.
If you work with a SPI device through a library, the CS pin switching usually performs by the library.