Heat a frying pan over medium-high heat. Add the olive oil and heat until shimmering. Add the onions and jalapeño and season with a pinch of salt. Cook, stirring occasionally, until onions are soft and translucent, around 5 minutes. Add the garlic and cook, stirring, 60 seconds. Add the cumin and oregano and cook, stirring, 60 seconds.
Add the beans and cook, stirring to coat, until they start to soften, around 3 minutes. Add water and cook, stirring to lift any brown bits off the bottom of the pan, until they form a loose paste. Using the back of a spatula, gently mash half of the beans. Taste for seasoning and adjust with salt as desired. Cover with a lid to keep warm and set aside.
Heat 1 tablespoon of olive oil in a separate frying pan over medium. Working in batches, fry the tortillas in the hot oil until golden brown and slightly crispy, around 1 minute per side. Transfer fried tortillas to a plate lined with paper towel to absorb excess oil. Set aside.
To the same pan, add ghee and heat over medium-high heat until melted. Crack in the eggs and cook to desired doneness. Transfer eggs to a plate and set aside.
To the same pan, carefully pour in the salsa (it may splatter), and heat until warmed through, around 60 seconds.
Spread a layer of beans over each tortilla. Top each tortilla with a fried egg, spoon over some salsa and sprinkle with cheese. Enjoy immediately.