Yes, you can. Go to import and change to your screenshots directory. Then select "Import Only"... restart the app and your default screenshot directory will be the new directory it watches for new screenshots.
Thank you for the detailed feedback. I like the idea of grouping certain screenshots based on tags and origin. I wanted to put out the initial iteration and see what works before putting in more time. I am also working on an extension that can interface with the desktop app to provide finer details about the origin of a screenshot. Also thinking about optional backup for folks who want it. Thank you once again and I'll be sure to update on the next iteration.