As this site is primarily about the ancestors of my descendants, what I've done is look at it from our perspective and created a branch for each of my grandparents and one for each of my children's paternal grandparents.
This means an ancestor needn't necessarily show in a branch with their surname. As an example, our ancestor Charles Moore, Royal New Zealand Fencible, is to be found in the GEAR & MOORE branch, not the MOORE & ASTON branch.