If you go for the File>Save option, this will give you an Affinity document. I would suggest Exporting (File>Export) the image to a JPEG or PNG for example, save it to a location and then import the edited file into iPhoto afterwards.
You can automate the process. First you have to set up iPhoto:
1. Go to iPhoto ▸ Preferences, Advanced tab, click on Edit Photos: dropdown and select Affinity Photo from the dialog.
2. Make sure *Use RAW when using external editor* is unchecked, otherwise iPhoto will lose track of the image since Affinity can't save directly the edits from the Develop Persona.
Now when you want to edit an image in iPhoto's Library, right-click on the image there and select Edit in External Editor. Affinity Photo will open with the image ready to be edited. Edit your image then do a File ▸ Save. Press the Save Flattened button (you have to save a flattened photo, since iPhoto doesn't support our native format (.afphoto) which is the format selected if you do a Save As). The image will be updated in iPhoto.
