Just because two animals have lived together a long time doesn't mean they'll be cooperative.
If one dog is particularly aggressive to the point it's harming the other you may want to consider re-homing one of the dogs. Your most aggressive dog would ideally be in a one-dog household.
If you are dead set on never giving one of the dogs to a new home (and I don't mean sending them to the pound, I know that could spell certain death to any dog particularly one that might have behavior problems or is older) or if you're not sure what you are going to do just yet you can try to reintroduce the dogs to one another.
Here's one way to go about it.
As a general rule of thumb for having two animals in the home you'll want to make sure they have their individual spaces with their own toys and their own food dishes that you don't leave out for them to become possessive over.
So that means when food time is over the dishes are taken off the floor, toys are put away, and even leashes are out of sight so that the dogs aren't fighting over the things they see as 'theirs'.
And as much as you might want both dogs to be close to you at night, putting their dog beds in separate rooms can help prevent late-night fights. Caging one or both dogs over night will also ensure they don't attack one another and you can leave a water dish out in the cages over night.
Make sure the cages are large enough for the dogs to turn around in and lay down, put their favorite bed in it and let them get accustomed to their respective cages before keeping them in over night. Be sure the cages aren't in a place that gets particularly hot or very cold or in an area that one dog is possessive over where the other dog would be likely to wander over to. It might be best to let the most aggressive dog chose it's cage first, let it become attached to that cage and then put the other dog in the remaining cage so that your possessive dog has already formed an attachment to the cage it chose.