The photos in the monthly projects and the manually imported photos are redundant. You can delete either of them.
Or since i have enabled Auto Import should I stop manually importing images?
You can either turn off the auto import and only import manually, or don't import them again manually.
The advantage of the manual import would be, that you could delete photos from the Photo Stream, before they are downloaded to your mac, so you do not have to delete the bad shots twice, on your mac and on your phone.