I have been able to do really well with my Dad's side, his family had been in the same area of Virginia/West Virginia since the early 1600s. Interestingly enough when I trace his mother's tree and his father's tree back all the way to the first family in America, it turns out that they are descended from a brother and a sister. Not that the brother and sister married, but that the lines came back together over 350 years later.
My mom's side is has been a little harder in some branches, but then I also have a royal branch and am a Mayflower Descendant on her side so that is pretty cool. Of course on her one side, her great-great grand parents were first cousins so my family tree turns into one branch. LOL
My tree allows for the parental relationship to be listed as biological or adopted and provides different branches for each. Makes it so much easier.