Yes, absolutely, you can learn your devices when in CCF mode. I 'learned' 6 different remotes this way and it works great.

You might be confused by this line from the PDAWin website.

"...You can enter "Learn" and RC5 IR codes. TV remote controller does not work with entered RC6 IR codes end predefined devices codes in ProntoEdit software. If you want to use RC6.... IR codes just learn these codes with your PDA."

This confused me at first as well. I still don't really know what it means. I don't think English is this person's first language. In any case, you should be able to learn and use codes from all your remotes.

Regards. Jay.