The best option is to completely cut out any rotted areas you find. Remove any dead or dying branches. Make all cuts with a slanted angle so water will shed off and not sit on any surface.
If the rot is invading the trunk, the will be very difficult, to save. Keep any mulch away from the bark of the tree as this keeps bark wet and softens it, allowing to disease to attack at that compromised area. Once disease/rot is into the tree, fungicides usually do not cure it. Contact a licensed arborist for a full evaluation and safety check of your diseased tree.