How to configure Dropbox to automatically delete the pictures from the phone that have already been uploaded via camera upload

There doesn't seem to be a way to do this at the time. Using Windows shortcuts is one possibility to make it as though the files are located in the same folders, however, it seems like it would get a bit complicated if there are a lot of folders.

There is a feature request for this exact issue, which you can vote on.

Other features you may want to look for is the ability to watch any folder, which you might be able to use in conjunction with your file system to create a limited set of folders to sync. Another one that might help is excluding certain file extensions, this would help if all the large files are of the same type (e.g. .exe, .avi, etc.).

I'm using the android app and I just go to the "Camera Uploads" folder and select "Upload here" from the menu.

You then get asked to select "Photos and videos" or "Other files". Select "Photos and videos".

Choose the photo you want to upload and select Upload.

If the file exists, it will ask if you want to replace the file.