I will preface this by saying that there is no such thing as "the" deep litter method, it's a whole bunch of different things and really no point in acting as if they're all the same because each person's approach will have its own unique pros and cons, its own unique benefits and disadvantages.
That said, MOST OF THE UNIVERSE that uses deep litter in some fashion or another does NOT use diatomaceous earth with it
This is a relatively newfangled concept, if nothing else because of availability.
You do not have to do anything different to use DE with deep litter than to not-use DE with it. I do not personally see much benefit (moisture and odor have much better, root-of-the-problem ways to control 'em) and the dust factor is not irrelevant for human or chicken health IMO.
Just experiment, see what works for you in your particular situation, then go with it