.NEF is the RAW file extension for Nikon, so no worries there.
When iPhoto imports your photos it copies them into the iPhoto library folder. When you edit the image in iPhoto, it either converts it to a jpg (the default) or .tiff if you've selected it in the preferences of iPhoto. iPhoto never (as far as I know) touches the actual original file and the original is kept in a folder something like "Pictures->iPhoto->Library->Roll 1->Originals" (note, that might not be 100% accurate since I moved my iPhoto library to an external drive and I'm just on my way out so I don't have time to confirm that right now
). Hope that helps
Keep asking if you've got questions