It's really up to you but I prefer to cover my enchiladas with aluminum foil while they bake to help prevent the tortillas from drying out and becoming hard and to also allow the sauce to become hot and bubbly. After they've baked for about 35 minutes, I then remove the foil, top the enchiladas with cheese, and bake for about 5 more minutes uncovered. Those final 5 minutes of baking uncovered perfectly melts the cheese and allows the top of the enchiladas to crisp up a bit.