I own 2 fans 1 in each bedroom, and the remotes for each run both fans / lights. How do I set the fans and remotes to be on separate signals and where do I find the documentation to do this?

You probably don't need a manual. Look for a set of DIP switches in the remote and correspondingly in the canopy. They should be set the same way.

You may want turn power off or remove batteries before changing the switches.

Try contacting, ceilingfan repair. He will probably be able to help you out.

You will have to change the frequency on one fan/remote set. See:

Ceiling fan remote controls - help and FAQ- Ceiling Fans N More