One of the important aspects of protecting your fist is in making a proper fist. You don't want anything that prevents you in doing so, this also applies for gloves as well.

It's important to wrap your hand's correctly, like Scrap says you don't want too much wraps going over your palms. It's just as easy to add extra hand wraps over your knuckles if it's long enough, or adding some preprepared bandages or towels over the knuckles. Tape can help to hold the wraps, and add strength to the wrist, but I'd be careful in how mine are wrapped because of the various official regulations. A good trainer usually knows best, and if they know the various regulation that differs from place to place that in itself can give you an extra advantage.

If you're knuckles are still sore but the swelling is gone you can start applying heat to speed up healing. You can use a bucket of hot water, or a hot damp towel. Don't keep it in there too long as to hurt yourself, and gently massage to help the blood circulate there.