JabRef is designed to facilitate your workflow.
You can select a subset of entries using the search bar. Within a library, you can organize your entries in a tree-like structure made of group and subgroups of entries.
You can add information to an entry using the entry editor, but JabRef can also complete the information for you. And JabRef takes care of the associated files (PDF, etc.)
Once your database starts to be large, some tidy-up may be needed. JabRef can check for the integrity of your entries, clean them up, detect duplicated entries, help you in merging 2 entries.
Hence, your database is always clean and up-to-date.