Hi Shan:
Please reference to the Chapter 8 system boot of MX6 RM
1. Please change the Boot_MODE{1:0] to 0x10 (internal boot mode) by switch thw SW1.
2. Please set the BOOT_CFG1[7:4] to 0x010x (boot device is SD card) by HW rework on J12 (Boot Mode Switches)
3. Please set the BOOT_CFG2[4:3] to 0x10 (boot from USDHD-3) by HW rework on J12 (Boot Mode Switches)
4. And please also reference the Table 8-15,for the detail settings.
Then you can check the SD3_CLK and SD3_CMD by scope for the boot device setting.
Best regards
Aven