Like most of us, you have more than one branch on your tree. You will want to keep the information separate for the different lines. How you do this is up to you. You can add a tab to the front page for each family name or you can make a header page with the name. What ever makes it easiest for you to find the information you want easily.
I print off a pedigree charts with the names already on them from my genealogy program and they become the front page of each section. I then place any documents or pictures I have found that relate to the people on that pedigree chart.in the pages behind them. Keeps it easy to find and neat. I also never only have one copy of anything. Ever since our house fire, I always make sure to have multiple copies stored in different places including in a container under the bed which is what saved mine.