Keeping dogs in the same household separated, even for short periods of time, can try the patience of a saint. But when it's necessary for safety and health -- to allow healing or stop aggression, for instance -- the keys to keeping your sanity involve supervision, control and planning ahead.
Keep sick or recuperating pets in their own area until they are cleared by the veterinarian. They should have their own room away from the other household dogs, with separate food and water. Place all dogs on leashes when you walk the ill or injured one outside to control everyone and avoid fighting or rough play.
Confine the dog to his crate or a smaller area of the house, such as a bedroom, for short periods of time when you cannot supervise him with other dogs. A dog's crate is meant to be a "safe" zone; allowing him downtime away from other canine stimulation can be beneficial. However, keep the other dogs away from his crate so that he does not feel he is the only one put on lockdown.
Place your dog in a fenced-in backyard where he can run and play to work off nervousness or aggression while away from the other household dogs. Spend adequate time playing with your dog in the backyard, as well; he should see this as a happy place to spend time.
Create a kennel in the backyard for the dog who needs isolated, if a long-term solution (such as for aggression) is required and a fence will not contain him. While a dog house and cable run will provide shelter and exercise, extremely aggressive dogs may require additional fencing to protect anyone or anything that comes into the yard.