My advice is
1) disable the SPI ROM and eMMC
2) boot from micro-SD*
3) enable the SPI ROM and eMMC
4) zero out both the SPI ROM and eMMC
5) install your operating system (with U-boot) to eMMC
*Many readily available micro-SD card boot images don't actually boot without U-boot or Tow-boot on the SPI or eMMC. The only one I can say for certain does is the DietPi one from the wiki. I have read reports of other operating systems that work, but I know for certain that DietPi does.
1) disable the SPI ROM and eMMC
2) boot from micro-SD*
3) enable the SPI ROM and eMMC
4) zero out both the SPI ROM and eMMC
5) install your operating system (with U-boot) to eMMC
*Many readily available micro-SD card boot images don't actually boot without U-boot or Tow-boot on the SPI or eMMC. The only one I can say for certain does is the DietPi one from the wiki. I have read reports of other operating systems that work, but I know for certain that DietPi does.