I have just lain the fabric on the dies without pre-cutting. I usually have enough room to fold the fabric on the side of the die. I will line up the raw edge just slightly past the die edge for strips.
I would also recommend Ebony Love's book, "The Big Little Book of Fabric Die Cutting Tips." She has lots of information in it. That's where I originally saw the suggestion for marking the dies with a Sharpie. I use the silver one on the black foam dies and black on the new grey foam dies. Even though you can see the blades somewhat, it does define them better. I also like her suggestion of marking the 1/4" around the edges to know how to center it better.
Just be careful where you grab the dies, I grabbed one across the blades and ended up cutting myself - not badly, but did draw blood.