I use a spreadsheet. I've tried paper, but I tend to misplace it, so a spreadsheet. I only use information from decent sources when trying to work out a conflict. I find it helpful to see all the information one one sheet. I'll head a column with possible parents and then place the children under them, provided there is a baptism or something naming the parents. My sister uses test trees, but I'm a spreadsheet gal.
A couple of things to note: A census record cannot reliably prove a relationship. Sometimes the wife listed is not the mother of the children, but the step-mother. This is not noted on a census. Some years the wife lists the number of children and those still living. That can be helpful. I hope you can find some marriage records listing the parents, that is often the best help.
I've been doing a lot of cleanup on Family Search. It is a lot of work.