Hi Kristian,
Without the resistor the BBB will always boot from the eMMC first, check section 5.3.5 of the BBB manual. The resistor does the same thing as pressing the "Boot Switch". Right now we don't use the resistor. You flash one microSD card with GLUED, and on the first boot you press the "Boot Switch" to boot from the microSD. When the boot process finishes, you mount the first partition of the eMMC, remove its contents and copy the files MLO and u-boot.img from the folder /boot. Afterwards, unmount the partition and reboot. This way the bootloader will reside on the eMMC and the operating system will reside on the microSD. GLUED upgrade scripts will then take care of updating the bootloader, no need to press the "Boot Switch".
Regards,
Ricardo martins