How do you hook up a handheld fan remote to a 3 way switch? There are a million wire ac in, what does it all mean?

The handheld remote receiver wires in between the fan and the power source. So you would hook it up in exactly the same way as the light that was previously controlled by the 3 way switch. Then you hook the other side of the receiver to the fan.

Ceiling fan lighting - Ceiling Fans N More