Hello,
I took down an old light fixture at the top of our upstairs. There were 2 Red, 2 green 2 black and 2 white and 2 more white with a black in a nut cap. I have 2 switches that both have a red, black and white wires. The ceiling fan has a light kit and it has a blue, black and white wire coming out the top of the fan. Any clue as to what all of these wires are? I sure appreciate your help, so will my kids.

Assuming the wiring was done correctly in the first place: black is hot, white is neutral, green is ground, and blue or red is used for connections from switches to lights which may be hot or cold depending upon the switch position.

Yokeman

My next question is there are 2 wall switches. They have 3 screws each. The one downstairs has a red and a white wire on the 2 gold screws that are on the same side, the black wire is on a copper screw on the other side
Upstairs is the black wire on a black screw and the white wire on the screw below it. On the other side is the red wire. This all comes into the ceiling box where 2 green wires are together, and 2 red and 2 black and the 2 white. The bad part is, there are 2 more white wires with a black wire with it connected together. Any idea what's going on there?

This is a 3 way switch circuit, both switches are called 3 way switches, used to control a light from two locations.

This wiring connection is very specific, and changes or mistakes will cause the switches not to work as intended.

Can you give me a clue about the wires that are in the ceiling where the fancy light used to be. I don't care if the fan has to be turned on by the chain. I just want this to work from the up or down switch. We really need the light for my son, he is scared of the dark. He's young! I really appreciate your help and expertise
The wire coming out of the fan are blue, black, and white. This is including the light kit.

Connect the black and blue from the fan to whatever wire the old light's black connected to. Connect the white from the fan to whatever wire the old light's white connected to. Connect all grounds together.

http://www.ceiling-fans-n-more.com/ceiling-fan-wiring.php

Thank you for all your help! I read everything and printed it all and I now have a working fan and light in the upstairs. Thank you all for your help :)