Hi,
This is highly board specific, but you might need to use MENDER_IMAGE_BOOTLOADER_FILE and MENDER_IMAGE_BOOTLOADER_BOOTSECTOR_OFFSET to instruct the mender-part-images.bbclass to embedded your boot loader files in the resulting sdimg.
I noticed the uboot.env generated is full of zeros, is that normal?
This is normal, this file is only used to calculate size and does not actually contain the U-Boot environment