I've been using/planning to use this technique for split level shots. By exposing AND focusing for both the under and over parts of the shot separately seemed an obvious place to exploit the joining of two images to create a greater whole.
I think it is important to keep the camera as close to the same position as possible between shots so that perspective is maintained and the image doesn't look too stuck together.
I used this technique (just using jpgs) for the split level image I used in my D100 Subal D10 review in Underwater Photography Mag's Feb Issue. You can quickly see the same image on my D100 pageclick here
I got plenty of mail about that article but no one has questioned the "integrity" of the split level! Although that may have something to do with the fact that it is probably the worst split level shot I have ever published! But with about a 4 stop difference in exposure between the under and over aspects (in the UK in January) I think the image is acceptable image that I could have never managed on film.