A default firmware image is embedded in the bootloader file boot.bin and can only be changed by updating the RCE core software.
The user controlled RCE firmware resides on the boot partition in a file named fpga.bit.
To change the user firmware, transfer your firmware bitfile to /mnt/boot and rename as fpga.bit.
To switch between the default firmware and the user firmware, reboot the RCE with the correct bitload option
reboot_rce -b 0 - Disable loading of fpga.bit and reboot with default firmware image
reboot_rce -b 1 - Enable loading of fpga.bit and reboot
Note, this behavior will be maintained across all subsequent reboots.