New ceiling fan has internal remote and wiring that is green black and white. My ceiling has black red white and green and goes to two switches. The ceiling fan has an upper and lower light and the upper light does not work. How should I wire?

White to white, green to green, black to black. Put a wire nut on the red. One of the switches, the one the black wire goes to, will have to be on for anything to work.

Why doesn't the upper light work?

I would recommend to check this article on ceiling fan wiring (http://www.ceiling-fans-n-more.com/ceiling-fan-wiring.php)

I recommend it to everyone.

Are the two switches together or at opposite ends of the room? This could be a three way switch OR it could be one switch for the light and one for the fan, we will know once you answer back