Combine soy sauce, lemon juice, 1/2 the chopped onion, onion slices, chopped garlic, and black pepper in a separate bowl. Pour marinade over the salmon; add the rest of the chopped onion, minced garlic, and garlic-pepper seasoning.
Cover bowl with the salmon and refrigerate, flipping fish over in the last 3 to 4 hours, 12 to 15 hours total.
Preheat an outdoor grill for high heat and lightly oil the grate.
Place salmon on the grill or on planks; top with the marinated onion slices. Cook until nicely browned, 8 to 10 minutes. Reduce heat to medium-low and cook until fish flakes easily with a fork, 3 to 5 minutes more.