How do I program my two remote control ceiling fans so the remotes operate each fan separately? Currently each remote operates both fans. They are Harbor Breeze fans with lights

Fan remotes and fan receivers has a series of very small switches (dip switch) inside each unit. Currently both fans have the identical sequence as the one transmiter. You need to open the canopy and get to one receiver and change at least one of the 9 switch setting and then make your second remote transmiter match that fan.

Yes. Sometimes the dip switches are in the motor or switch housing.

Ceiling fan remote controls - help and FAQ- Ceiling Fans N More (http://www.ceiling-fans-n-more.com/ceiling-fan-remote-controls.php)