I am trying to connect a ceiling fan that has a remote control. The remote transmitter has on one side a white and black cable. On the other side a black, white and blue cable to connect to the fan. My ceiling has two switches. One switch has a red and black cable and the other has a white and black cable. The wires from my ceiling are red, black, white and neutral. Where do I begin?

Ok, what wires come from the fan?

Are you trying to change the switches?

Ceiling fan wiring - Ceiling Fans N More (http://www.ceiling-fans-n-more.com/ceiling-fan-wiring.php)

The fan and one side of the remote box have blue, black and white. The other side of the remote box has a black wire and a white one. The ceiling has a white, a red and a black coming out of it.

That part's easy. Match the fan to the side of the remote box. The other two from the remote box, connect to white and black from the ceiling. If that doesn't work, switch the red and black from the ceiling.

So, How do can I cap off the other wire? Red wire. Sorry for the dumb question.

Serious. How do I cap off the wire?

Just put a wire nut on it by itself.