If you're using a whole squash or sweet potato and need to cook it, do that first following any recipe to roast or steam in bite-sized chunks. You'll only need a cup or two cooked.
Set the temperature of your oven to 425 and spread or spray a little bit of oil on a rimmed baking sheet.
Finely mince your onions and allow to soak in a little lime juice or apple cider vinegar for 5-10 minutes to take away a little of the sharp bite but not the flavor. Drain excess liquid.
Set out a few flour tortillas on the baking sheet, and then start to assemble your ingredients on just half the tortillas: beans, roasted squash, corn, any other vegetables, minced onion and jalapeños, a small dollop of salsa and finally cheese. Just make sure not to overpack them-- just a few spoonfuls of filling is plenty.
Fold the opposite half over top of the ingredients and press down. Paint a little oil on top, and bake for 10-12 minutes until cheese is melted and tortilla has crisped up.
Cut into wedges and serve with salsa, sour cream, cilantro or avocado.
You can also do this in a cast iron skillet on the stove top. To get a panini press effect, once stuffed, place a second smaller cast iron skillet on top of the quesadilla while cooking.