Atomic resolution images of clean Si(001)-(2x1) and the monohydride phase, Si(001)-(2X1)H were investigated using scanning tunneling microscopy at various sample-tip bias voltages. At a sample-tip bias of -1.9 V, each dimer of the monohydride phase shows two protrusions 3.3 angstrom apart separated by a minimum 0.12 angstrom deep, while clean dimers show a single protrusion per unit cell. Monohydride dimers appear lower than "clean" dimers, with apparent height differences ranging from 1.9 angstrom at -1.6 V to 0.65 angstrom at -3.0 V sample bias. An analysis of the apparent height and spatial distribution of tunneling current within each dimer can be used to unambiguously discriminate between clean dimers, monohydride dimers, and vacancy defects. This methodology is applied to study the distribution of hydrogen on Si(001) surfaces during chemical vapor deposition using disilane, revealing segregation of the monohydride into nearly isotropic islands.