I use the CF slot for RAW, and is my primary card.
I use the SD slot for JPG, and I keep a Eye-fi in it... the idea is that JPG is there for safety, and when I want to, I can enable the Eye-fi, for iPad previewing during a shoot. I also have the back-screen review set for this card, and have my sharpness/saturation/etc. set on my picture style to match what I typically do in ACR, so I get a better idea of what my photos will look like later.
When I empty the CF card for the day, I format both cards in-camera before storing the camera.