Set the config switches like this:
Next plug the custom flash cartridge into the GB/GBA slot of the cartridge reader. You'll find the "Flash GBC Cart" option under the Game Boy sub-menu.
Supported cartridge types are the DIY MBC5 Cart following the design by Reiner Ziegler and the MBC3 and MBC5 cart by jrodrigo both with a 29F016/32/33/08 type of flashrom.
Also supported are the HDR MBC30: https://github.com/HDR/MBC30-Flashcart
And HDR GameBoy Cam: https://github.com/HDR/Gameboy-Camera-Flashcart
These are all found under the "29F016/32/33 Cart" selection.
There is also a more general CFI option that could work with more carts if they have a compatible flash protocol.
Once you have selected your flash cartridge type it will ask for a file and then flash said file to the cartridge.