I recently started to use Aperture 3 to manage all my iPhone photos as well as my other photos. The first few times I synced from my iPhone I tried in vain to find the “delete after import” button but couldn’t find it (this button was present in iPhoto and I swear it was there in Aperture 2). Turns out, if you want Aperture to delete your photos after import you’ll need to launch Image Capture with your iPhone connected. Check the “Delete after import” button and you should be good to go. For those of you who haven’t used Image Capture, you can use this to delete all photos from your iPhone as well. Image Capture is a great utility app and it’s included for free on the Mac (look in Applications->Utilities). Keeping your iPhone photo albums neat and tidy speeds up many apps that use the photo library. I’ve heard that it also speeds up the iPhone backup process.