Hello. Sorry I didn't answer sooner, I only noticed the question now. You enable a custom empire to spawn as a fallen empire by allowing it to spawn in the game. In the empire selection screen check the little eagle icon next to the empire's name. If it's grey click it once, if it has a lock, click it twice, and if it's just colored then you're set.

However, the empire can only spawn if it has an ethic that matches one of the possible fallen empires: xenophobe, xenophile, spiritualist, materialist, or gestalt.

Gestalt also only works for machine empires. It doesn't work for hiveminds. Not unless some other mod added a hivemind fallen empire.