I do this with Aperture for Mac, which isn't free or even currently supported, but my basic technic should work with most of the common free digital photo organizers. The key point in this is file naming.
1) photograph or scan your print
2) include all useful information in the filename, most photo programs allow you to batch rename files. The system I use is Date (YYYYMM) + film + camera + lens + developer + time + index (negative number). An example filename would be " 201707 HP5 plus - Minolta XTsi - Minolta 50_1.8 - HC110 dil B 5 minutes - 05.TIFF" Since I store negatives in chronological order, I would just look at the date at the beginning of the filename to know where the negatives are located. It seems somewhat awkward, but, by using VueScan software, I can set up the scanning process to automatically created the filenames. You could include as much information in the filename as you want, just be careful to avoid illegal characters in filenames. I generally replace "/" with "_".