No matter the amount of data you are handling, organization is key to prevent data from being lost, misunderstood, or be becoming incomprehensible. Following file naming conventions can make your data easier to access and understand quickly. Stanford University Libraries have described some best practices for file naming conventions, as does this video tutorial from the State Library of North Carolina. Make sure future researchers (and yourself) can then understand your data by composing a README.txt file, creating a codebook, and writing a data dictionary.
After all the hard work you went through to gather your data, the last thing you want is to lose it. The best practice for saving data is the 3-2-1 Rule: Store three copies of your data on two different types of media with at least one stored in an offsite location. For more information, check out this tutorial from Explaining Computers on data backup.
Citation managers can be even more helpful than just organizing PDFs of articles. They can handle a variety of data types, such as newspapers, books, and even datasets! This Drexel library guide explains how to cite data from a repository.
Know you need to use a citation manager, but are unsure of which one would suit your needs? This Drexel library guide provides a comparison of different software and online tools for managing your citations.