Alpha dog behaviour

Question
I have a 3 year old Shepherd, who is very well mannered and never had any problems with him.
We recently got another shepherd who is now 8 months old. Also male.
I've noticed my older dog growls at him, he will go hide, there will be a trail of urine.
A few times they have fought, with the younger dog underneath on his back. Lots of growling and barking, no biting.
Is this the older dog just showing his Alpha dog dominance?
Should I intervene in the fighting?
Should they be kept seperate?
Is this a phase?
They are together during the day in the dog run.
Most of the time they seem to be ok, licking each others mouths?
What do I do?

Answer
When adding a second dog, it is best not to get a second one of the same sex.  Usually it isn't too much of a problems unless both have a strong dominance drive.  Once one has clearly claimed the dominant position, they may play together OK.  Here is a link to a picture of my shepherd playing with a visiting Lab, http://www.photolocker.net/images/Labman/gretchenandellaplaying.jpg  Your 3 year old is at the age where many dogs lose their interest in the puppy play.  Part of what you are seeing could also be the older dog telling the younger one enough, leave me alone.  

The problem could get worse as the younger one matures, and decides he is old enough to challenge the older one for leadership.  If both are neutered, it will be less of a problem.  Two intact males outside in a run, and a female in season upwind, could mean problems.  Neutering them also reduces the chances of cancer later in life.  

It will also reduce problems if you are clearly top dog, and they contesting for the second spot.  The key to most behavior problems is approaching things using the dog's natural instincts.  Dogs see all the people and dogs in the household as a pack with each having their own rank in the pack and a top dog.  Life is much easier if the 2 legged pack members outrank the 4 legged ones.  You can learn to play the role of top dog by reading some books or going to a good obedience class. A good obedience class or book is about you being top dog, not about rewarding standard commands with a treat. Start at http://www.dogsbestfriend.com/  As part of being top dog, and to help sort out what they are doing, look at http://www.dogbreedinfo.com./topdogrules.htm