Set up your desired controller layout by using the dropdowns to select which buttons on a standard Xbox-gamepad layout should map to the given Dreamcast button.
Click the desired download button for either picotool upload or for a microSD card.
Save the controller mapping config file to the 'pico2maple' folder on your Pico2Maple's SD card.
While Pico2Maple is in BOOTSEL mode, use picotool to load the mapping onto the device using the following command:
picotool load "pico2maple-mapping.bin" -o 0x103FC000
Precompiled picotool binaries are also available.