At the moment, I don't have a fully written guide on how to load the software- but I am working on it!
The best way to load the software is either through a FlashCart, or through Mutliboot. Personally, I would suggest utilizing a Wii with Homebrew and FIX94's gba-link-cable-rom-sender to send the ROM over. After the ROM has been sent over, you can insert the Gen 3 game and continue from there!