How do you know you have dead spots? I have sand in 3 tanks now and I've seen nothing to indicate trouble. And, some anaerobic zones are essential for good plant growth and good health in the aquarium. Read my article on bacteria, I cover this in the bit on substrate.
I would just leave it alone. However, 2-3 inches is sufficient. I reset my 115g about a month ago with playsand, and I put in 110 lbs (50 kg) which is 2 bags. It evened out to about 2.5 inches. I built up areas along the back with slabs of basalt to have deeper areas for the Echinodorus cordifolius, E. major and E. bleherae. There's about 1.5 to 2 inches elsewhere. I've no intention of touching it.
I have Malaysian livebearing snails too.
My other two sand substrate tanks have been running for a year, about 2 inches sand depth.