In the end I think it is easier to keep it all together. Although some people do split via their parent (2) or grandparents (4). But the farther back you go you may find interrelationships that make having one tree more feasible.
To me it is easier to keep track of one tree even with lots of people. Even though it means from day to day one part or another of your tree needs to be ignored. Also it is much better if you ever plan to do a dna test.