Directed evolution is frequently applied to identify genetic variants with improvements in a single or multiple properties. When used to improve multiple properties simultaneously, a common strategy is to apply alternating rounds of selection criteria to enrich for variants with each desirable trait. In particular, counterselection, or selection against undesired traits rather than for desired ones, has been successfully employed in many studies. Although the sequence and stringency of alternating selective pressures for different traits are known to be highly consequential for the outcome of the screen, the effects of these parameters have not been systematically evaluated. We developed a method for producing a statistical modeling framework to elucidate these effects. The model uses single-cell fluorescence intensity distributions to estimate the proportions of phenotypic populations within a library and then predicts the changes in these proportions depending on specified positive selective or counterselective pressures. We validated the approach using recently described systems for metabolite-responsive bacterial transcription factors and yeast G-protein-coupled receptors. Finally, we applied the model to identify biological sources that exert undesirable selective pressure on libraries during sorting. Notably, these pressures produce substantial artifacts that, if unaddressed, can lead to failure of the screen. This method for model generation can be applied to FACS-based directed evolution experiments to create a quantitative framework that identifies subtle population effects. Such models can guide the choice of experimental design parameters to better enrich for true positive genetic variants and improve the chance of successful directed evolution.