When you try to upgrade the controller using the GUI, two partitions are shown. One partition will say [**default boot**] next to the description. That is the default boot partion. You should upgrade the opposite partition.
The document says to upgrade the non-boot partition so that you can easily switch back to the partition you were running without uploading an image if there were any issues. Many people are confident in the image they are upgrading to and ignore this. It is mainly a time-saver if you have to revert.