We present an improved model for excess variance spectra describing ultra-fast outflows and successfully apply it to the luminous (Lbol ∼ 1047erg s−1) low-redshift (z = 0.184) quasar PDS 456. The model is able to account well for the broadening of the spike-like features of these outflows in the excess variance spectrum of PDS 456, by considering two effects: a correlation between the outflow velocity and the logarithmic X-ray flux and intrinsic Doppler broadening with vint = 104 km s−1. The models were generated by calculating the fractional excess variance of count spectra from a Monte Carlo simulation. We find evidence that the outflow in PDS 456 is structured, i.e., that there exist two or more layers with outflow velocities 0.27–0.30 c, 0.41–0.49 c, and 0.15–0.20 c for a possible third layer, which agrees well with the literature. We discuss the prospects of generally applicable models for excess variance spectra for detecting ultra-fast outflows and investigating their structure. We provide an estimate for the strength of the correlation between the outflow velocity and the logarithmic X-ray flux and investigate its validity.