I maintain two different family trees: one maternal, one paternal. Breaking it down this way helps me to keep track of all the data more efficiently, but it can still become a bit overwhelming, particularly when trying to remember to follow through with my intentions to research the siblings of my direct ancestors.
In an attempt to try to improve this process, I'm working on creating spreadsheets for my direct ancestors that lists their basic information (dates and locations of birth and death, parents, spouse, children, and siblings). I've started with the Stephenson line, but I'm not yet sure how this experiment is going to turn out. In all honesty, I'm not sure if having a spreadsheet is really going to help me to keep track of everyone any more efficiently than my pedigree charts do, but it's worth a try.
My hope is that I will wind up with an Excel workbook that is easy to navigate and that helps me keep better track of all the different ancestors I would like to research.