I'm not quite sure what you mean, but how the scanning works may depend on the software. I run my scanner with the Apple app "Image Capture." With that app, I choose or create a folder for my scans and suggest a name (like Book 01, for instance.) Then Image Capture scans an image, names it Book 01- 1.jpg, and saves it in the folder I specified.
When I'm done, I drag the folder containing the new scans to the Photos app, and Photos goes through the import process, checking for duplicates and such. If I have sub-folders, Photos keeps those intact when importing.
There are lots of possible ways to do this, but this works for me. I end up with the originals still in that folder, and I'm comforted that I have that as a backup in case I mess something up.