For iPhoto '09 I used (parts of) the below workflow. Somewhat tedious, but it worked.
I haven't tried it on iPhoto '11 yet, but maybe it still works (possibly with some alterations)
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"Single Library Approach"
In this method I use a single iPhoto library to contain both RAW (NEF) files and their associated JPEGS.
(a) Set iPhoto->Preferences to use Capture NX2 as external editor.
(b) Set iPhoto->preferences to send RAW files to this editor.
(c) Set iPhoto->preferences so double clicking on photo opens editor.
(d) Make smart album in iPhoto for "file type is RAW", so after an import any RAW files show up in this album.
(e) Create alias for iPhoto modified photo directory and place on desktop. (This is accomplished using finder by browsing to username/pictures/iPhoto Library, then right click and select "show package contents", then right click on the folder named "modified" and select "make alias". Then move this created alias to the desktop and close the iPhoto library. What you have here now is a pointer to your internal iPhoto library to the place where iPhoto keeps every modified image. Whatever you change here changes in iPhoto permanently, so be careful.
(f) Connect a memory card and all photos are automatcally loaded into iPhoto. This may be a mixture of RAW and JPEG shots, it doesn't matter.
(g) All RAW files imported show up in the RAW smart album.
(h) open this album and start editing by double clicking on the first photo. It opens in NX. Make any adjustments you want, then in NX click "save". This saves your updated NEF file, then immediately after this click "save as" and browse into the modified alias created on your desktop and find the subdirectory containing the image you are modifying and save there. It should ask you "overwrite?" to which you respond "yes". If it does not ask to overwrite you are in the wrong directory, so it is actually a useful check. You can find the correct name of the directory by looking at the "open recent" tab of NX. The first file listed is the original NEF you are editing so the directory path to save to will be the same
except the word "original" should be replace by "modified".
ℹ Close the image in NX and go back to iPhoto. Immediately iPhoto realizes it has a new image in "modified" and updates it's corresponding thumbnail to match this. The type of image is now reported as "JPEG (From Nikon RAW)" and it inserts the keyword "Raw" as well. At this point both the NEF and the corresponding JPEG are in iPhoto, but iPhoto no longer considers the original file and it dissapears from the Raw smart album (which is actually really usefull because it helps keep track of how many RAW files you have left to convert). Don't worry though, your original NEF is still there in iPhotos library, and all you have to do to get back to is is select "revert to original" or "reprocess RAW" in iPhoto. At this point you can re-edit if you like and repeat the process, but the two files (NEF and JPEG) will spend the rest of their lives together in iPhoto.
