How do I delete photos from iCloud once they have been moved out of downloads folder?

I have 600+ photos that show up on my iPhone 6 and in iCloud photos. iCloud is installed on my PC and is downloading new photos regularly. I usually move these manually to sorted folders elsewhere on my PC. The photos still show up in iCloud and on my phone though. How do I go about syncing the folder back up to iCloud once I've moved them out of the downloads folder?