CM3 has 2 SDIO interfaces, namely SD0 and SD1.
If using CM3 with 4GB flash, SD0 is used to talk to the flash chip and boot from and can not be changed. This leaves the SD1 interface available for WiFi or additional emmc/sd card.
If using CM3L SD0 interface is available to the user and can be used for SD card or emmc for booting. This also leaves SD1 available for WiFi.
For more information refer to compute module data sheet, page 11, 18 and 19. https://www.raspberrypi.org/documentati ... T-V1_0.pdf