The FPGA bitstream alone is what is normally configured by the ChipWhisperer-Capture software. This bitstream is always the most up-to-date, since it's automatically reloaded by the computer every time you power cycle the ChipWhisperer-Capture. The SAM3U firmware however is not automatically updated, but it tends to change less frequently.
[[Manual SAM3U Firmware Update]]
==== Checking Firmware Version ====