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There are two bits of software which make the Satiator run: the firmware and the menu.
The firmware is flashed to the Satiator itself. The firmware is where the magic happens - hooking itself into the Saturn's CD block, emulating discs, et cetera. New firmware is loaded by putting a
satiator.fw on your SD card; see the instructions below for more detail.
The menu is stored on the SD card, in the file
menu.bin. The menu is the code that runs on the Saturn to list all your games and so forth. There's no special procedure to update the menu - just drop the new
menu.bin on to your card.
Firmware is updated by loading a new
satiator.fw on to your SD card, and then powering on the Satiator, either via USB or turning on your Saturn. You should then wait until the LED displays three green blinks, indicating that flashing has completed. Then, you can cycle power again to boot into the new firmware.
If you interrupt power while it's still flashing the new firmware, you can get stuck with the LED showing a different blink code (red red green). If this happens, check out the troubleshooting instructions for an interrupted firmware update.