Here’s one thing I am doing to organize my research: I used TreeSeek.com to generate two 9-generation PDF pedigree charts. One chart is from my FamilySearch Tree, the other is from my RootsMagic file, which originated from my Ancestry tree. Both trees are large with plenty of errors, so I highlighted where there are discrepancies in names and vital events.
I compare each person in each file, and when I have reconciled the errors, I click on Tools > Stamp to stamp the person in the chart with a little “approved” sticker. I like being digitally organized and not having to deal with file cabinets full of paper! How are you organizing your research?