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Prepare a grill for cooking or heat a saute pan over medium heat. Grill or saute chicken breasts over medium heat until cooked through.
While chicken is cooking, spread 1 tablespoon Walnut Pesto on each of 4 slices of the panini rolls and 2 tablespoons Chipotle Aioli on each of the other 4 slices.
Remove chicken from grill and build each sandwich by placing a chicken breast on top of the bread with Walnut Pesto, then a tomato slice and 2 pieces of cheese, 1 tablespoon Three-Onion Marmalade, and topped with the bread with Chipotle Aioli.
Place all ingredients in a food processor or blender and combine on high for 2 minutes or until smooth. Transfer to a 13 by 9-inch non-reactive baking dish or other flat container. Add chicken breasts to dish, cover, and marinate in the refrigerator overnight.
Preheat oven to 350 degrees F.
Spread walnuts on a small sheet pan and toast in the oven for 5 to 7 minutes. Place all ingredients, except oil, in a blender and process until smooth. Slowly add the oil and continue to puree for 1 minute. Set aside.
In a large skillet, heat the oil over a medium-high flame and lightly brown the garlic, about 1 to 2 minutes. Add the yellow and red onions and cook until wilted. Add the pepper, sugar, and vinegar, lower the heat to medium, and cook until the onions are translucent, about 5 minutes. Add the green onions and cook for 2 minutes. Remove from the heat and set aside.
Mix mayonnaise, garlic, and chipotle puree in a small bowl until well combined. Set aside. Refrigerate if not using immediately.
*Cook's Note: Chipotle puree can be found in small cans, sold as "chipotle peppers in adobo sauce" at major supermakets.