Wiring 6 pin SD Micro to CANBED FD

Check the embedded development board you are using, find the pins that support the spi protocol and connect them according to the rules, and use the relevant driver or write it yourself.

CS (Chip Select) is the way chooses which peripheral to converse with, so there must be a separate one-to-one connection from some output pin on your board to the CS pin on each peripheral.

The other SPI signals you will need at least one of are MOSI (Master Out Slave In) and MISO (Master In Slave Out). They are the channels for the actual data being passed.