As JG has explained it is normal heirarchy behaviour, if you have a bossy little boy it will go on for a while as already said it is most usual for the bitch to end up ruling the roost, he will eventaully learn his place.
You can't prevent it, it is all part of two pups growing up together, but you can minimize the effects, what starts the niggling and fights, food, toys, getting the leads, attention, or does the male just start play launching at your girl which then turns into a free for all? All can be solved by knowing what starts them off and distracting them from each other if you can be vigilant enough to read their body language, have a toy or game ready to help them to loose interest in each other, feed in different areas if this causes problems, and lead one whilst the other is busy, just learn to work around them.
Don't seperate for noises, snarles and teeth baring, only if a real bite should happen, try not to get too scared, mostly it will just be noise and body language very rarely will a dog and bitch actually draw blood, they need to have these little fights to find their pecking order. I know it sounds frightening, but if you check there should not be any injuries.
Only seperate if things get out of hand, as already said with age it will calm down, two pups together causes so many problems but with understanding you will get through it, and so will they.