Say I have two HDDs already installed on the primary IDE controller, and two CD/DVD drivers on the secondary... Can I remove one of the optical drives and put a third HDD in its place for temporary files copying?
Yes, there's nothing special about the second channel. You should consider just getting an external USB2 or Firewire drive bay if it's a temporary thing though. They're not too expensive and they save a lot of hassle. You never know when they'll come in handy.
You should also consider having your hard drives on seperate channels to begin with if you do a lot of copying between them.