The creation of well-understood structures using spectral hole burning is an important task in the use of technologies based on rare-earth ion-doped crystals. We apply a series of different techniques to model and improve the frequency dependent population change in the atomic level structure of thulium yttrium gallium garnet (Tm:YGG). In particular we demonstrate that, at zero applied magnetic field, numerical solutions to frequency-dependent three-level rate equations show good agreement with spectral hole-burning results. This allows us to predict spectral structures given a specific hole-burning sequence, the underpinning spectroscopic material properties, and the relevant laser parameters. This enables us to largely eliminate power-dependent hole broadening through the use of adiabatic hole-burning pulses. Although this system of rate equations shows good agreement at zero field, the addition of a magnetic field results in unexpected spectral diffusion proportional to the induced Tm ion magnetic-dipole moment and average magnetic-field strength, which, through the quadratic Zeeman effect, dominates the optical spectrum over long timescales. Our results allow optimization of the preparation process for spectral structures in a large variety of rare-earth ion-doped materials for quantum memories and other applications.