I had a boring hour and decided to make a small graph which might help many beginners to understand the different steps of the boot procedure of the Beaglebone.
Hopefully this explains when and why something is booted from the MMC or the eMMC.
It's available here:
As U-Boot is highly configurable, this just describes the current procedure and isn't complete (in regard to what all is possible by changing U-Boot or uEnv.txt). It also doesn't describe how the ROM boots from USB or the UART (serial).
And, just in case, please don't ask me questions about that. Read the SRM (System Reference Manual), TRM (Technical Reference Manual) and the U-Boot documentation/source if you want further answers.